That's actually one of the hardest things I've tried to overcome (after realizing it) in the last few years: Music that's connected to some kind of memory/event/show/movie/etc. will constantly make me think about its associations rather than my work at hand.
I've noticed the same thing about myself lately. I even stop listening to some of my favorite songs because they arouse negative feelings or images of places I dislike.
I found it sometimes to be a positive effect. Many times when I felt bad I listened to my favorite touching/sad songs while working - they tend to suck the emotional entropy out of me and help me focus on task at hand, while my emotions get 'aligned' with the song.
Why overcome it? That's one of the most beautiful things about music, no?
ah, but I believe it's entirely appropriate. Not to turn this into a Lost discussion, but one of the main themes of the show was redemption. The island was a place where all of the everyday crap was gone and the characters could step back and say, "what the hell am I doing?" I believe that's the intention here as well.