Religious supervisor wants to thank god in the acknowledgements
On a coauthored paper, it's perfectly reasonable for the acknowledgments to specify who is thanking whom when it's just a subset of the authors, and this is not uncommon (e.g., "X and Y are grateful to the A Institute for hosting their visit" or the like, when author Z wasn't actually there).  This is the approach Ritz suggested in the comments, and I'd strongly recommend it.  For example, in this paper one author thanks God, without including the others.

I'm sure nobody would hold this against you personally, and I can't really believe anyone would discard or disbelieve the paper because of the acknowledgments.  It might indeed get some attention: even in mathematics, I've heard people comment on an author's tendency to thank God (nothing negative, just a "gee, that's unusual"), and I can imagine it might get more attention in areas where religion is more contentious.  However, I don't think you need to worry that your career will suffer because your coauthor thanked God.