Evidence from the first episode (spoilers)
In the very first episode we see Pernell be lead to Shane as the person who raped Jocelyn. When Shane is killed later on by KD and he confesses to the crime, we should have all known from that moment that Pernell wasn't hallucinating and god was really talking to him. How else could he have known that it was Shane? There was no evidence linking him to the rape. Otherwise, the police would have figured it out.
I think it's kinda annoying how the show kept making us think that maybe Pernell was really crazy and god wasn't speaking to him but, it's obvious that god was helping Pernell, and that his reward would be having PJ wake up. I pretty much knew that PJ would be saved at the end since Pernell was doing so much to make that happen.
This is a show where god most definitely exists and for some reason, he cares about the son of a corrupt judge who is morally bankrupt and a lousy father. I'm not a religious person at all but, I can appreciate what this show had to say about god and having the visions be true was a nice twist even though it was obvious from the very beginning.