score:6
It is completely okay. I do similar things all the time, although the two passports I hold are both visa-free in most of the places I visit.
The Greek official will not care whether you have a stamp from Turkey in your passport. She or he will be concerned only with stamps from Greece and other countries in the Schengen area, to determine whether you have ever overstayed your visa. Assuming you have not, there will be no problem.
Of course, if the Greek official does ask about your travel to Turkey, or whether you have Iranian nationality, you should tell them that you are an Iranian national, and if it seems they want documentation of that, show your passport.
In general, you should volunteer as little information as you need to, but always give any information that they ask for.
I would add that I once entered Turkey with some Bosnian/Canadian dual nationals who did not have their Bosnian passports. Turkey is (or was then) one of the few places that Bosnians can go without a visa. I was traveling on a US passport, and my visa fee was something like USD 15 or 20. The Canadians, entering on their Canadian passport, had to pay a fee of $60, if I recall correctly. I think the disparate fee amounts are based on the fees that Turks have to pay for visits to the country in question.
My friends regretted that they had not brought their Bosnian passports; you'll save a decent amount by remembering your Iranian one.