I'd stay away from the ointment because unneccessarily medicating is never advisable. In this instance, it could lead to evolving a resistant strain of bacteria. It would kill off some/most/all of the flora in the areas it touched, but since it would only touch the lowest six or eight inches (15-20cm) of the colon, and essentially no digestion goes on in that region, probably no problem in that regard (there is a small amount of water resorption happening down there, but even that mostly happens higher in the large intestine).

I doubt your anibiotic ointment would have much effect on a virus, since most of them are specifically anti-bacterial. If it's dual-use anti-bacterial/anti-viral, it should say so on the label. I don't think many viruses are found on the skin; I think they're mostly active in the bloodstream, which a topical agent wouldn't touch.

Sounds like a topic for norcod!