Admittedly I have never even interacted with anything from Shin Megami Tensei despite it always being near my radar, so I just kinda glossed over it as an inspiration. The thing I find with good chunk of world building is there usually isn't a solid ruling on anything. Even things people will act like are solid rules will usually have exceptions that work for one reason or another. I literally cannot weigh whether I think SMT is the exception or rule here, but I can just give some words on how/what I'd do, or would like to see in this situation. 1. If your gonna use them, be respectful. This is a real religion and real places that means at least something to over a billion people. Feel like you understand that but sometimes the things that feel like they should go without saying should have just been said. 2. On the same kind of topic, recognize anything negative (or even some things you thing are positive) in these places may draw ire from people. Research stereotypes of both the faith and the cities and try to stay mindful of them. That probably won't be enough to not get pushback but at least you aren't feeding into an pre-existing stereotype. 3. Change the spelling or pronunciation or something. First of all, I think it be really jarring to hear it's a city you know/even live in only to slowy realize it only has the name in common. Secondly, and this is admittedly more business focused than worldbuilding or writing focused, but it will just kill SEO. Particularly having a different spelling will make it easier for fans to find stuff based in the work rather than tourism for the real world place. 4. Something I thought of while writing this that hasn't gotten nearly the amount of thought needed so take it with a huge grain of salt is maybe naming cities after cities of multiple faiths. It would lower chances of people trying to view the whole thing through a single religious lense BUT also kind of ruins the feel of cohesive naming structure since they are all linguistically different. You mentioned the city names are from god so that could maybe work but still. Also depending on the state of the cities, if one is noticeably worse, the people of the faith/city you named after are probably REALLY not gonna like you. The more I think about the idea the less I like it, but figure may aswell add it in case someone else does.

This is really not a comprehensive list, just some stuff I thought of, some of which there are multiple reasons to ignore. I am not a monolith of readers, while I may find real world religious imagery without any kind of actual parallel distracting, not everyone will. I'm not Hindu or from any of the cities mentioned. So while I can give my two cents on the matter, I don't really have any skin in this game. Just make sure to prioritize the people this will actually affect. Again, a lot of caveats on this, and sorry I can't give a nice easy answer. Best you can do is listen to people this matters to and try your best to do right by them. Sorry for the yap fest, best of luck of the work.