1) What's with the animosity towards missionaries... I mean, most Christian churches send their missionaries to do actual good AS WELL AS spread the faith. And for the most part they don't knock on doors (Jehovah's Witnesses are NOT representatives of Christiantity (though they claim they are). They are a cult, or a separate religoen, depending on who you ask), telemarket, etc.
2) The missionaries know they are going into a hostile environment over there. They're not going to be a problem unless we make them one, and most are prepared to deal with whatever problems they may encounter (prepared to survive is another story, but they're missionaries not soldiers. The hazards come with the territory).
2) The 'New Iraq' is supposed to be a democracy, where people are free to choose their way of life, INCLUDING religeon. The extremists will fight that no matter what, but for progress to be made, these extremists must be rooted out. The best way to do this is to introduce choices (especially formerly 'verboten' items) and see who breaks the law to oppose said freedom of choice. When they do, it's time to practice our book-throwing skills.
4) We're allowing the sale of booze, and many other things that will PO the muslim radicals. Iraq is not Iran, and there are enough different groups, and enough of a 'Islamic-in-name-only' (similar to the USA's 'Christian-in-name-only') population to make containing the radicals doable...
5) That said, we shouldn't do anything special for the missionaries unless it coincides with US interests in Iraq. The government shouldn't support them (unless they're working on a needed humanitarian mission), but shouldn't discourage them from going either...