The thing is, those lines are part of a scene where the Scoobies are standing around confused trying to work out what the heck is going on. Giles certainly doesn't know everything about the prophecy; he apparently was unaware that Angel would have a role in it at all. So my reading is, he's speculating.

I actually think it's more like 'Where The Wild Things Are'. Riley and Buffy chose willingly to have sex in that episode, but supernatural forces started feeding off the mystical energy they were giving off and wouldn't let them stop. Afterwards, the two of them were embarrassed about what happened because of the side-effects, but didn't feel any angst over the fact that they had sex. Substitute "the universe" for "restless ghosts" and "Angel" for "Riley" and it seems like the same deal here, only on a larger scale.