Yep, that bugs me too. A lot. I watch the movie now and instead of seeing Gandalf of the story, I see the actor who hates the God behind all the good in the story. Fatal distraction.
McKellum's Gandalf-fight with the Balrog was (in my mind) the best symbolic portrayal of Christ fighting demons, descending into the pit (of earth, hell), dying, coming back resurrected and transfigured, that I have ever seen. He comes back --- at the turn of the age --- so radiant that Aragorn, Gimli, and Legolas bow and kneel in homage.
So our old atheist can appreciate --- in a shadowy way ---- the nobility of priestly and Christly realities.
Let's pray for him.