Quote 1
None of them ever accused me of being responsible for what had happened to Phineas, either because they could not believe it or else because they could not understand it. I would have talked about that, but they would not, and I would not talk about Phineas in any other way (12.14).
This is Gene's moment of greatest loyalty to his friend. By treating Finny's death honestly, he reveres him in a way he never did when Finny was alive and Gene had to protect himself.
Quote 2
The moment was past. Phineas I know had been even more startled than I to discover this bitterness in himself. Neither of us ever mentioned it again, and neither of us ever forgot that it was there (8.108).
Phineas and Gene treat this outburst the same as they do Gene's earlier confession at Finny's house. Their friendship is predicated upon a suspended reality they build together. Or something else.
Quote 3
It struck me then that I was injuring him again. It occurred to me that this could be an even deeper injury than what I had done before. I would have to back out of it, I would have to disown it (5.75).
There are two ways to interpret this passage. Either this is one of Gene's greatest moments of honesty (he would rather live with his shame than hurt Finny by revealing the truth), or it's yet another moment of justification (he pretends he doesn't want to hurt Finny in order to recant the truth and save himself from persecution).