He doesn't *hate* being at the Academy. In fact, he grows to love it. But really, at heart, he's a ship captain, and that's what he wants. Not everything can have a purely happy ending. HOWEVER, if Pike hadn't made the decisions he made, whether or not Kirk was around, if Pike hadn't risked himself, the Earth would have been destroyed. I think he's okay with that consolation prize.

But yeah, the guy definitely developed a bond with that ship. The Enterprise kinda does that to folks. But remember... he found Jim the same night he found the Enterprise. There's something poetic about it, and I could see him thinking about that when he realizes that he can't stay on as Captain. But still... the universe kinda trampled on him a bit.