I think it's a matter of weighing pros and cons. First ask yourself, why are you using that real city in the first place - versus some different real city? Does it matter if your novel's city is on the west coast versus the east coast? What is it about THAT city that drew you there? If you know someone there, maybe ask them. If it was for some unique feature(s), stick with it, but if you were simply looking for a somewhat generic rural town, why not make one up? "Metropolis" works for Superman.
If the issue is more that you're second guessing your ability to create a fictional city, ask yourself why you're hesitant there. Is it because you don't know where to put City Hall? There's nothing wrong with a real place as a frame of reference. And depending on the story, there's the "parallel universe" creative liberties. (You say there's no church there? Well, in my story, those buildings burned down years ago.) There's also the possible danger that a real place will slow you down, as you keep looking up details -- a friend of mine puts in <street> as something to look up later for that reason.
As for me, I made up an Ontario town to use as a setting for my T&T time story. While I'll likely shift the location to Ottawa eventually, that's because I need a university, and I live here. But that may be because I don't want to fall down the rabbit hole of constant research.