I believe that the writer means that what "began to do its subtle damage" was not the promise of losing weight but the premise, i.e. the context. The fact that we would be running on a Marathon began to seem more important than the fact that he would be merely losing weight. He could lose weight by running around his block but instead he chose a Marathon and at this point the writer starts to realize the monumental effort and the overall context of the race.

This is what I gather from the given phrase. 
I hope that I helped you.