Did the Marshall plan only give back a part of what was taken?

I would argue just Western Germany's post war economic achievements verses Eastern Germany's troubles refute this premise fairly comprehensively. The argument comes down to the US, British, and French were terrible; but they were certainly a lot better than the soviets. If this is a perfect world type argument then it becomes uninteresting. Beyond that, I can think of five real world holes in this premise.

Firstly you can't eat a patent. You can't go to work in a patent. Nor will a patent keep the lights on or the communists from radicalizing all your people who have no jobs, and no food. Nor will a patent protect your boarders for 50 years and provide unquestioned security. These are all things grants, loans, material donations, and soldiers the United States provided assisted post war Germany with.

Secondly and most importantly, this kind of Zero sum game, thinking reflects the punitive thinking which saw Germany crippled economically after the first World War. Perhaps you could make a case the allies owed Germany for technology, equipment, and infrastructure lost during the war. (It would have to be a very good argument however because frankly their is more legal precedent even inside Germany for dissolving the country and selling all it's citizen into slavery). The Allies likely would have responded with the Billions and Billions in costs that they incurred in putting down Germany's aggression. After the allies were done, perhaps the relatives of the 60 million folks who died in WWII, might all sign up for a class action lawsuit and stripped down Germany financially so all they had left was tooth picks. Suffice it to say, even if many German achievements did in fact become the foundation of post war Allied efforts into these sciences; Germany still ended up way ahead financially of where they could have been if the Allies wanted to take their cases before some sort financial tribunal/court, and tally everything up. The reason the allied went dutch on their costs for WWII weren't entirely altruistic either. The crushing debt and economic costs Germany were saddled with after WWI, were thought by many to be a significant cause of the second world War and the rise of Nazi's. The allies who were very concerned with the spread of communism were very motivated to ensure all of Western Europe could see light at the end of the wartime recovery tunnel. Especially Germany who they wanted to be a future friend and ally.

Thirdly nations don't own patents, individuals do. and the program you are eluding to, Operation Paper Clip, targeted those individuals, as well as the technology. So the United States weren't content in just grabbing all the V-2 rockets it could get its hands on, they likewise recruited the scientists who had built them.

Fourthly, Why stop at the Marshal Plan? The Allies, did a lot to shore up Western Europe's (and Eastern Germany's specifically) economy after the war. Not just the Marshal Plan.

• From July 1945 through June 1946, the United States shipped 16.5 million tons of food, primarily wheat, to Europe, (not just Germany though). It amounted to one-sixth of the American food supply, and
  provided 35 trillion calories, enough to provide 400 calories a day for one year to 300 million people. As long as we are counting pennies, who do you think paid for all that?
• Along with the million U.S Soldiers the United States kept in Western
  Europe to guard it's security from the east as Western Europe got back on it's feet for nearly the next 50 years.

Fifthly and lastly, The Marshal Plan wasn't a gift. It was partially grants, but mostly it was loans. Loans which E. Germany had to pay back, which they did in 1971(final payment). So the premise that it somehow in part repaid for technology "looted" from Germany is a false one.

The Marshal Plan was financed by the United States to the tune of 13 billion dollars in 1948 money (over 130 billion in 2017 dollars), allowed many countries economies ravaged by war to rebuild their infrastructure on the US dime. You are correct that East Germany got about 11% of the overall package or about 1.4 billion. That's the simplified definition. The more complicated definition was mostly it was loans, and mostly the folks who ultimately received the money were US businesses. In 1948 if you wanted to buy things to get your economy rolling ( heavy machinery, mills for steel, production equipment ). The United States was you most likely source. So not only was the Marshal Plan very good for Europe, It was very good for the United States too. That's what we call good business. It should not be confused with charity, a gift, or some sort of guilty conscience war reparations.