1. A little humor - "Now, Mr. So-and-so, you know there's no politics and religion at work! Are you tryin' to get me in trouble?" This approach depends a lot on the patient's personality, the situation, etc.
2. Redirect - make it about the patient again. "I am not religious, though I can see your faith is important to you and helps you. What can we do facilitate your religious practice while you are in the hospital?" Except maybe not so officious sounding, lol.
3. Find some common ground (which is my favorite, personally, as I think it nearly always exists). For instance, I had a patient say the other day, "I can tell you're a believer, aren't you?" She was reading the Bible, so I just said with a smile, "I'm not religious, but I do love Ecclesiastes chapter 3. What's your favorite passage?" We talked for a few minutes, I did my assessment, and there was no problem at all between us.