So maybe, it's possible, he didn't despise Islam?
A man who thought of himself as a "true" Christian, in that he believed Jesus brought the best moral code to humanity, a man who had to deal with the Barbary pirates and who had to compromise in the signing of a treaty with dubious wording so non-Muslims wouldn't have to pay Islamic tax? Jefferson was no fan of Islam, believe me. He studied law, including the Qur'an as a system of laws, but I don't think he gave it a lot of consideration for the very simple reason that he didn't have to deal with it on home soil. He didn't keep the Qur'an by his bedside and memorize it. It was just extraneous study material to him. He was more concerned with arguments between Christian denominations - irritated by them, really, because he thought the disagreements were ruining Christ's real message. Although there were those of his time who did know enough about Islam to discuss it and to be rightfully fearful of it, I don't think Jefferson was an Islamic scholar. Rather, I think he approached it with some amount of naivete and a sense of it being "far away" and thus not our problem. If it had become an issue on American soil, I think he would have become obsessive in studying and refuting Islam because the laws of Islam are polar opposites from our Bill of Rights and our Constitution, and therefore, against everything he believed in.
Interestingly enough, this article was just posted. You may find it interesting.
Thomas Jefferson, Ben Franklin, John Adams and James Madison: Young America’s Fight with Islamism
http://www.freerepublic.com/focus/f-news/1761891/posts