I thought Sympathy for the Devil was a great choice of music for the boat level and fits the feel of the game wonderfully. The themes of both the song and the game fit together very well and it adds a nice special touch to the game.
As for killing people to a nice rock and roll sountrack, yeah I do agree that can be a little disturbing, but a game set during the Vietnam war should disturb you slightly at least once. If you plow through a historical conflict (or even a fictional conflict) without a pang of guilt or disturbance the developers haven't donje a good enough job, or maybe theres just something strange with you.
EDIT: I think having Eminem play over the second half of the credits kind of sucked. I guess the themes worked well, but rap feels too out of place for a Cold War game and took me out of the experience. Rap didn't work for CoD4 or GoW either.