Quote 1
It is a curious thing, do you know, Cranly said dispassionately, how your mind is supersaturated with the religion in which you say you disbelieve. Did you believe in it when you were at school? I bet you did.
I did, Stephen answered.
And were you happier then? Cranly asked softly, happier than you are now, for instance?
Often happy Stephen said, and often unhappy. I was someone else then.
How someone else? What do you mean by that statement?
I mean, said Stephen, that I was not myself as I am now, as I had to become. (5.3.86)
The declaration that Stephen’s transformation was necessary indicates that perhaps the person he is now is who he was somehow destined to be all along.
Quote 2
A restless feeling of guilt would always be present with him: he would confess and repent and be absolved, confess and repent again and be absolved again, fruitlessly. Perhaps that first hasty confession wrung from him by the fear of hell had not been good? Perhaps, concerned only for his imminent doom, he had not had sincere sorrow for his sin? But the surest sign that his confession had been good and that he had had sincere sorrow for his sin was, he knew, the amendment of his life.
– I have amended my life, have I not? he asked himself (4.1.14)
Even at the peak of Stephen’s rigorous religious discipline, he still has doubts that he has done enough. This is typical and unsurprising – after all, even if God himself showed up and said "Hey, Stephen, enough already," he would probably still have doubts. This is the old Stephen we know and love, not the passive, unquestioning dude we’ve seen most of the time in this chapter. His nagging dissatisfaction is what lets us know that Stephen’s destiny doesn’t lie in the religious life.
Quote 3
– Then, said Cranly, you do not intend to become a protestant?
– I said that I had lost the faith, Stephen answered, but not that I had lost self-respect. What kind of liberation would that be to forsake an absurdity which is logical and coherent and to embrace one which is illogical and incoherent? (5.3.100)
Stephen still values Catholicism over other religious systems; he recognizes it as "an absurdity" but still holds it above Protestantism. At least Catholicism is a "logical" absurdity. This whole distinction seems a little absurd.