Yes originally under the Articles of Confederation(March 1, 1781) which was the first attempt to form a union by the 13 colonies. Absolutely the "Union" was intended to be originally a loose confederation where the federal government had no revenue streams except those which unanimously were agreed upon by the states. This article was so weak the federal government could not even pay the interest on it's war debt, much less defend itself with a standing army. The failure of the Articles of Confederation is the reasons why James Madison and George Washington advocated for the passing of the stronger document with a stronger federal government, including an executive and the right to tax; the Constitution. Madison being a primary author, and Washington being the documents highest profile supporter, and President of the Constitution convention(1787).

Even after the Constitution was ratified(June 21, 1788) this question wasn’t settled. The simple truth is the founding fathers didn’t agree. Jefferson believed any state which freely entered the union was free to leave if it suited then. Patrick Henry, George Mason(the only founding father who refused to sign the Constitution), and Monroe in his younger days agreed with Jefferson. George Washington, Madison, John Jay, and Alexander Hamilton disagreed. The latter three wrote as much in the Federalist Papers saying a division of the union would mean 1000 years of war as two nations would follow the same history as European nations which fought 1000 years of war over economic, religious or cultural reasons and was to be avoided at all costs. This was the motivation for the north fighting the south in the civil war. To preserve the union. It became about slavery for the north later in the war.

Original Answer: Actually you are incorrect. The House of Representatives in the original Constitution was always elected by popular vote. The peoples house. The Presidency, Senate, and Supreme Court were appointed by representatives of the people and not by popular vote itself.

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The original Virginia Plan envisaged that both branches of the federal legislature would be directly or indirectly accountable to "the People." In the end, however, the Convention determined that the states would be represented in the Senate and the people in the House of Representatives.

The term I think you are looking for is Republic. Today we like to mix the terms Republic and Democracy. The founding fathers of the United States were very clear on the differences. The founding fathers didn't agree on much, but they all agreed they were creating a Republic and did not trust Democracies. A democracy killed Socrates. They were very concerned with a democracy's ability to protect the rights of a minorities from the tyranny of the majority. Concerns that the people would be influenced to act against their best interests, or those of their fellow citizens by smooth talking charlatans. That is why they created a constitutional republic, with a bill of rights and never intended to create a democracy.

After the French revolution, and the mob inspired blood baths which followed. The popularly supported murdering sprees, the founding fathers believed they were wise to fear unchecked popular mandates from the people.

That's why originally senators were appointed by state governments, and Presidents were voted on by senators, and only the House of Representatives with it's short terms in office were entrusted to the majority vote. It's also however why the house of representatives was entrusted with the power of the purse, the right to tax, the right to write the budget.

The first popular vote for President was recorded in 1824, and that was also the first of five Presidential elections where the winner of the popular vote failed to win the election. John Quincy Adams became President in 1824 and not the winner of the popular vote Andrew Jackson.

(*)In truth the founding fathers were very concerned with any abuse of power of a federal government.

The US Supreme Court has repeatedly ruled NO.

What you're describing is similar to Compact Theory, the idea that the United States was formed by an agreement between the states. This idea comes up a lot with advocates of states rights to reign in federal authority. It's an idea that's been kicking around since the Constitution was ratified and has been used to justify all sorts of things.

Constitutional theorists and the US Supreme Court have roundly rejected Compact Theory stating that the United States is formed by the people. The issue was legally put to rest after the civil war. Here are some examples.

In 1793 Chisholm v Georgia, Georgia claimed that as a sovereign state it had immunity from lawsuit. The court ruled 4-to-1 that in Article 3, Section 2 of the US Constitution states gave up their sovereign status and federal courts have the right to hear disputes between states and their citizens. The Eleventh Amendment later undid this ruling, but the legal precedent remained that the states were no longer sovereign.

In 1816 Martin v. Hunter's Lessee resolved the issue over who had ultimate authority over state legal decisions: state or federal supreme court. Virginia state supreme court used an interpretation of a US treaty that the US supreme court disagreed with. Virginia argued its supreme court had ultimate authority over cases originating in its own state court. The US supreme court disagreed. Justice Joseph Story wrote in the unanimous decision...

The constitution of the United States was ordained and established, not by the states in their sovereign capacities, but emphatically, as the preamble of the constitution declares, by 'the people of the United States.'

In 1819 McCulloch v. Maryland, the US supreme court ruled over a Maryland law requiring all bank notes not issued in Maryland to be taxed targeting the Maryland branch of the Second Bank of the United States. One of the arguments used by Maryland was that "The powers of the general government, it has been said, are delegated by the states, who alone are truly sovereign; and must be exercised in subordination to the states, who alone possess supreme dominion." Compact Theory. Justice Marshall rejected this idea reiterating that it was the people, not the states, who ratified the Constitution, and thus the people, not the states, who are sovereign. In the majority opinion, he directly addressed the issue, writing...

In discussing this question, the counsel for the State of Maryland have deemed it of some importance, in the construction of the Constitution, to consider that instrument not as emanating from the people, but as the act of sovereign and independent States. The powers of the General Government, it has been said, are delegated by the States, who alone are truly sovereign, and must be exercised in subordination to the States, who alone possess supreme dominion.

It would be difficult to sustain this proposition. The convention which framed the Constitution was indeed elected by the State legislatures. But the instrument, when it came from their hands, was a mere proposal, without obligation or pretensions to it. It was reported to the then existing Congress of the United States with a request that it might "be submitted to a convention of delegates, chosen in each State by the people thereof, under the recommendation of its legislature, for their assent and ratification."

This mode of proceeding was adopted, and by the convention, by Congress, and by the State legislatures, the instrument was submitted to the people. They acted upon it in the only manner in which they can act safely, effectively and wisely, on such a subject -- by assembling in convention. It is true, they assembled in their several States -- and where else should they have assembled? No political dreamer was ever wild enough to think of breaking down the lines which separate the States, and of compounding the American people into one common mass. Of consequence, when they act, they act in their States. But the measures they adopt do not, on that account, cease to be the measures of the people themselves, or become the measures of the State governments.

From these conventions the Constitution derives its whole authority. The government proceeds directly from the people; is "ordained and established" in the name of the people, and is declared to be ordained, "in order to form a more perfect union, establish justice, insure domestic tranquillity, and secure the blessings of liberty to themselves and to their posterity."

The assent of the States in their sovereign capacity is implied in calling a convention, and thus submitting that instrument to the people. But the people were at perfect liberty to accept or reject it, and their act was final. It required not the affirmance, and could not be negatived, by the State Governments. The Constitution, when thus adopted, was of complete obligation, and bound the State sovereignties.

It has been said that the people had already surrendered all their powers to the State sovereignties, and had nothing more to give. But surely the question whether they may resume and modify the powers granted to Government does not remain to be settled in this country. Much more might the legitimacy of the General Government be doubted had it been created by the States. The powers delegated to the State sovereignties were to be exercised by themselves, not by a distinct and independent sovereignty created by themselves. To the formation of a league such as was the Confederation, the State sovereignties were certainly competent. But when, "in order to form a more perfect union," it was deemed necessary to change this alliance into an effective Government, possessing great and sovereign powers and acting directly on the people, the necessity of referring it to the people, and of deriving its powers directly from them, was felt and acknowledged by all. The Government of the Union then (whatever may be the influence of this fact on the case) is, emphatically and truly, a Government of the people. In form and in substance, it emanates from them. Its powers are granted by them, and are to be exercised directly on them, and for their benefit.

The final nail in the coffin of Compact Theory was Texas v. White in 1869. The case hinged on whether or not Texas had seceded from the Union. The court ruled that Texas did not have the power to leave the Union because the Union is not a compact between the states, but something more. Chief Justice Chase wrote in the 5-to-3 majority opinion...

When, therefore, Texas became one of the United States, she entered into an indissoluble relation. All the obligations of perpetual union, and all the guaranties of republican government in the Union, attached at once to the State. The act which consummated her admission into the Union was something more than a compact; it was the incorporation of a new member into the political body. And it was final. The union between Texas and the other States was as complete, as perpetual, and as indissoluble as the union between the original States. There was no place for reconsideration or revocation, except through revolution or through consent of the States.

...Considered therefore as transactions under the Constitution, the ordinance of secession, adopted by the convention and ratified by a majority of the citizens of Texas, and all the acts of her legislature intended to give effect to that ordinance, were absolutely null. They were utterly without operation in law. The obligations of the State, as a member of the Union, and of every citizen of the State, as a citizen of the United States, remained perfect and unimpaired. It certainly follows that the State did not cease to be a State, nor her citizens to be citizens of the Union.

You can read up more about Compact Theory in the answers to Was the secession of the Confederate states illegal? (spoiler: it was). In particular JimZipCode's answer.

According to Klarman, and Maier the founders explicitly addressed this in the Constitutional Convention, and rejected a confederation.

To me there are two questions within your question.

1. Was the intent of the US Constitution to be a confederation or not?

2. Why the indirect electoral techniques?

Although you connect them together in a thesis (Is #2 evidence of #1), they are not quite that closely related.

For #1 - the US was very explicitly not to be a confederation. The Articles of Confederation had failed, and the failure was accelerating. The new nation was to be "of the people" - there was a direct relationship between the people and the new government. In the Articles, the members of the government were the states in confederation; in the Constitution the members of the government were the people. This is why the Constitution was submitted to ratifying conventions in every state - the states were not given the chance to vote on the new government, and when the notion was suggested, it was rejected. So the new government was of the people, not of the states. Klarman mentions that at one point they realized that if the government were of the states and if one of the states were to ignore an obligation, the only recourse would have been war; if the government were of the people, and one of the people were to ignore an obligation, there were better options.

With respect to #2 - one of the signs that the Articles had failed was an increase in populism. Shay's rebellion was the worst, but in pretty much every colony there were movements led by common, ordinary people to obtain relief from inconvenient laws (particularly debts). They wanted paper money and high inflation. (inflation is generally good for the debtor). The political classes were perplexed, and perhaps horrified by the notion of shopkeepers and apprentices using political activity to obtain short term advantage without any consideration of the long term consequences. Therefore the new government was constructed to control and limit the power of populism. Indirect elections were used to remove the prizes of government from strictly popular control. (Klarman is probably a better read on this topic).

In both cases, I'm simplifying complex topics.