I’m not a Jehovah’s Witness, and I’d be a bit taken aback at someone ending a phone conversation with “God bless you” too. I certainly wouldn’t shun the person, but I’d wonder. I think it’s a bit different than saying “bless you” when someone sneezes. First of all because the way most I know end a telephone conversation is with some variant of “goodbye” or “talk to you later” so the speaker has gone outside the more common social conventions to one specifically mentioning a god, whereas with someone sneezing the only common responses seem to be “gesundheit” or “bless you” neither of which specifically mentions a god.
FWIW to the OP, the other day at work I gave “Season’s Greetings” cards to each team member specifically thanking that person for their contributions during the year and a gift selected for that person. One person on my team at work does not celebrate Christmas and has a significant other who is Jehovah’s Witness. I didn’t want to leave his contributions ignored, but also didn’t want to force acceptance of a “Christmas” gift, so in the end I gave him a thank you card, and a gift in plain wrapping. He seemed happy with that.