I'm not sure how much influence actual researchers have on choosing their projects either. One can always quit, but I'm not sure what sort of leeway there is to say "not this project, but I'll work on that one next door". I'd guess that it's not a unique situation for them to contend with since many intellectual types have qualms about militarism. The question is whether they're desperate enough for scientists that they'll bend, or if they're jaded enough to just go and find someone who will do the dirty work. I'm hoping the fine print in the contract they'd have me sign would be a bit more detailed, though it is security-clearance government-obfuscation level stuff so it may not.