Wolverine, up to a certain point, was bred as a weapon of war. Built bottom to top, on what they already had to work with, for maximum viciousness. It's very implausible, to me, that you use someone like that for the nice stuff. You use him for ops so black they're infrared, like this.
That said: in real life that village would have been, if for no other reason to instill terror, arbitrarily firebombed, profession of "No VC" or not, and obviously they knew where it was and what was there. They already had plenty of means to do that. Nuke is unnecessary here. Not in Latin America, where you did NOT have full-scale war weaponry being overtly used, and besides, the point of Nuke was a satire of Rambo, combined with a commentary on the difference in character of American war now vs. Captain America's day. Which, of course, is kind of a lie already, but a legitimate story point. I think all we needed to know about Nuke, Frank Miller already said. This sort of conspiracy view with this guy starts to really stretch credibility.
But I can easily believe Wolverine being this way. We're talking about a guy who is well known for going into psychotic fits, for one thing. His personality isn't so much complex as schizoid.