Maybe Ultimecia made him do it for funsies, maybe her mind control just meeses up his head too much, Seifer raped Squall when he got him imprisoned at the D-District Prison. Seifer subconciously knew what he was doing was wrong but he was too fucked up to care.

Bonus: they have some kind of intimate relationship before (maybe friends with benefit etc).

Bonus bonus: the two of them dealing with the aftermath.