well, part of it was the fact that she was going to end up in the same position as those girls because she doesn't have the physical strength or any sort of training to go up against them, and once she throws the pail at them, she's out of weapons. (I mean aside from eye-scratching-out and stuff.) She did end up falling off a cliff.

I also don't think Kyouya would have actually raped her.

Anyway, I ship them more in spite of that scene, but also viewing that scene as an important one--I mean, it happened--in showing how Haruhi deals with him. And how he reacts to that.