The prof then argued to us that these men are great thinkers and don't make the kinds of logical errors that you hear about in basic logic courses. Therefore, if it seems like he's making such an error, it's because we don't understand him, and are not taking his position sufficiently charitably.
Sadly, however, I do believe he's mistaken on that account. We are often well-motivated, emotionally speaking, to make logical errors. They are pervasive and difficult to root out of our thinking, that is why we study them, and why they are so dangerous. To suggest that anyone is immune to making such errors is absurd. And Descartes was certainly highly motivated to believe in god of a particular variety. He wrote a book he deliberately did not publish in his lifetime because he found the Church rejected the heliocentric view of the universe (a discussion of which was contained therein). And circular arguments, particularly in complicated arguments, are often difficult to root out. It's easy to forget what are assumptions, and what has been shown.
And though there is an accepted convention that corresponds to the idea of "perfect", it does not imply that perfect means anything more than "better (making fewer errors) than me, and better than anyone I know". We cannot conceive the kind of geologic time, so it would be just as impossible to conceive of a being that only made an error once every 50 million years... that is still not perfect; however, if you believe that the universe is less than 6000 years old, it would certainly seem to be. And it is a common error among those not accustomed to dealing with very large or very small numbers to distinguish this from infinity or zero. So, I have to ask... what does Descartes mean by "perfect" really, and is his definition logically coherent? It's the same problem most modern theologian have.