Short CircuitShort Circuit (1986) film has the US military as the villains, though it's a kids movie and I don't believe there are any deaths. You are definitely rooting against the military here.
Bringing in more violence, though it's probably overly broad, but there are a number of US Civil War movies where the enemy is still American. Glory is the first one that comes to mind.
Another possible answer, and it's a mini-series not a movie, would be TakenTaken (2002). At a high level, the protagonists are Alien's and 'good' people while the antagonists are military members following orders and those issuing the orders.