Well, I happen to like shounen ai and implied yaoi. Not the hardcore stuff mind you, but I read shounen ai and yaoi fanfics, and from what I've heard of Gravitation, it's a good story, mostly no worse than many other animes except for one scene in the OVA.
Of course, if you personally feel convicted or that it's wrong to watch it, don't. However, I don't believe that watching shounen ai or implied (not hardcore) yaoi anime is forbidden to all.
IMHO, all sin is the same. A favorite anime of a lot of people around here (including myself) has a main character who is a drunk and a heterosexual pervert (despite what the yaoi fanfic writers say) yet we don't roundly denounce it because of those things-they are incidentals to the main story and the character himself, just as the same-gender relationship between Yuki and Shuichi is incidental to the love story and to the characters themselves.
My point is, if we can like characters like Faye, Vash, Sha Gojyo, etc, and series like Cowboy Bebop, Trigun, and Sayuki-why are we forbidden from liking characters like Yuki and Shuichi and series like Gravitation?
Oh, and who says Gravitation couldn't have some morals in it despite the relationship? Even Cowboy Bebop portrays morals (albeit from a negative perspective, in showing bad morals and their end), and a lot of people here (including me) would claim that Trigun is somewhat of a morality play. . .so. . .what prevents Gravitation from having some morals despite one morally questionable thing in it as well?