Good write-up. Your daughter's science teacher is a sneaky bastard. He should not be trusted.
I tend to agree with your son's History teacher. The thank you note should simply thank the speaker for his time. Simple courtesy.
It would have been best if he had questioned the speaker in class so that the debate could have been presented to your son's classmates, however I do understand shyness. Perhaps your son could include a list of questions to the speaker with his thank you note (which would show interest in the topic without insulting the speaker), and suggest that he answer them on a return visit (or to the History teacher). Such as:
(a) is the Islam concept of "peace" the same as the Western or Christian concept of "peace"?,
(b) why are nearly all of the terrorists in the world Muslim?
(c) why are all of the world's present conflicts on the edges of Islamic civilization?
(d) why was Margaret Hassan beheaded?
I have a couple to add:
-Why are honor killings allowed in their culture/society?
-Are women treated with respect in this culture?
-Of the countries rated as "bad" (or lowest) regarding quality of living, technical advancements, etc., why are the top 7 of 10 the countries that have muslims as their majority?
I have more but this is a few.