Thesis: Hannibal fell in love with Will even harder because, not after, but because of Will‘s betrayal.
There is this perfect wonderful boy you‘ve become utterly obsessed with ever since laying eyes on him for the very first time. In season 2b Hannibal looses himself within the utter humanity that the promise brings to, very possibly, have his wildest dreams come true: this perfect boy is not only becoming your friend after you thought you‘d lost that friendship, he sees you for who and what you are, accepts you, and wants to join you. Imagine the unbearable elation he must have felt when Will brought him Randall Tier, cooked with him, I mean, no wonder Hannibal was loosing his mind.
Now this man betrays you. We all know Will devastated Hannibal (and I think Hannibal was both surprised and not surprised about how strongly he felt), but he also stepped from a place above all mankind, a place right beside Hannibal, to a place above Hannibal. His very own cruel God. Not someone for Hannibal to shape, to guide through his Becoming just how Hannibal sees fit, but someone better, higher, someone out of his manipulative reach. I think he fell all the more for him because Will refused to be taken in, how Hannibal wanted to take him (and how a part of Will wanted to be taken). Because, as all mortals, he realised he was truly powerless before his God. Will would either come to him, or he wouldn’t have him at all. And that ruined Hannibal entirely.