I don't think its unintentional at all, but you are correct that it does that (point with bright neon that the universe has meaning and everything is connected, etc), but that doesn't make its argument about faith any less interesting. He should have had it, but did not. He failed to humble himself before the universe and was shown the error of his ways.
Alternately, it was all coincidence, and he chose to interpret it as God. Faith isn't about the unknowable, but the un-understandable. The way we make sense of things, putting together various bits of reality in a coherent narrative we tell ourselves about the universe is an act of faith. In the end, Gibson constructs his reality in a way that is useful to him, that makes him feel better and gives him the ability to fight off aliens or whatever. It's not God beating him over the head: the bits were there all the time, Gibson just never assembled them until the end.