I'm pretty shocked UFC would let him go considering his win over Woodley.
I think it was one of two situations;
Him and the UFC accepted this was the best for him right now and left the door wide open for a return. He's incredibly young, if he storms through Bellator, UFC can re-sign him with fresh momentum and they get the joy of knowing Bellator is left with the guys he beat. Makes financial sense for both Rory and the UFC if it does play out that way. He gets paid what he's worth as a fighter, and the UFC doesn't have to do it until they think he's profitable again.
The other is what I feared, the UFC now being owned by a talent agency has cemented the shift from sport to a star-driven reality tv. The new owners probably looked at nothing but social media metrics and what he was asking for, and wouldn't even negotiate. He just doesn't have the personality you can sell out of a cage. If that's what made this happen it's essentially s statement saying "It doesn't matter how good you are if we can't sell you outside the cage". And that's fucking scary.