the guy has been on his own forever and has put Octavia before him forever.

This is a very good point. Bellamy has been shouldering a significant burden since he was very young. He's had to come to terms with standing by and allowing bad things to happen or putting himself last because that's what had to be done to protect Octavia, given their fraught situation on the ark. His Sister's Keeper is such an important episode for understanding not only Bellamy's mindset but also how this behaviour he's now having to unlearn has built up, by necessity, over a lifetime. Not for him the happy 'privileged' childhood on the ark that allowed Clarke to develop into a logical, intelligent leader.

The one time he took a risk to try to give Octavia some happiness on the ark, it went horribly wrong and he got her locked up. I'm not surprised he is deeply unsure of himself. I'm not surprised his reflex is to fall in behind others sometimes and let them do the intellectual lifting between what's right and what's wrong.

The episode where Clarke took the knife from him to mercy kill Atom was perhaps the first time anyone's took a burden off his shoulders in his life. His attitude towards her changed from there. And Day Trip was when she started to understand him better too, and told him he was a good person who could make good choices.

But you can't unlearn a lifetime's worth of reflexive decision making in a few months, especially when the person who started to coax him out of this left him behind. That's not either of their fault, but Mount Weather devastated both of them.

I think he accepted her leaving after Mount Weather, and did his best to get on with things. But her choice to stay in Polis with Lexa really hurt him. That was where his faith in Clarke took a nosedive. He was left without the person he'd trusted to be his moral compass.

I'm not surprised Pike managed to manipulate Bellamy, and quite quickly too... he was in a position of being incredibly vulnerable to it after that latest round of grounder betrayals.