Hmm. I don't think I applied to any rival football schools. My alma mater is is I-AA (or now Div. 1, Championship Subdivision), participating in the Colonial Athletic Association as of next season. I don't believe I applied to any schools who participate in that league. As for schools I otherwise hate for sports purposes, I only applied to two, and I was rejected from both (damn you Jesuits!), so I guess I've avoided the conflict of interest.
If I got into Penn, I'd root for their basketball team and football team, except for when they played Villanova. Having two teams that could potentially beat St. Joes every year, however, would be a VERY enjoyable experience for me.