Wow I think I finally get it!
I always took Sam at face value in this movie; though he never said it directly, he is ex CIA and since the end of the Cold War has become a nomadic gun for hire. He even says at one point he's just working for a paycheck. Well, I caught this movie on TV last night, haven't seen it in a while...always really loved it, though if I had any one complaint it would be how it gets a little too convoluted in the last half hour or so.
Annnyway, at the very end, when Vincent is chasing Seamus and Sam goes and talks to Diedre in the car, he says something like, "Don't you see, I never left. I am here for your boss." Well, it was like a lightbulb turned on for me - Sam still was an active CIA agent!! It was all a setup to get (what I assume to be) IRA boss Seamus out in the open and taken down. There is even a newscast at the end that tells us an IRA faction has negotiated with the British government. Sam then gets in a car *driven by his CIA contact* (who I just also noted was the same guy who Sam asks for help in finding Gregor) and drives off into the sunset.
I've seen this movie a lot, and now feel like an idiot for totally missing an integral part of the story. Just felt compelled to acknowledge how oblivious I was to one of my favorite movies.