if they owned the land how would you stop em?
Ya mean if I was the city and I wanted to stop the Orthodox church from going back up?
First I'd try to get the land re-zoned. A phone call from the mayor's office to the zoning board usually does the trick. In this case of the Orthodox church being rebuilt, that may not work. That land has been used as a church for decades, so it'd look bad to suddenly claim that location isn't suitable for a church.
Second, I'd try the ol' carrot and stick. I'd offer a big cash payoff if they move (hey, it isn't my money I'm spending, so I'd be generous) coupled with threats of legal action, condemnation, eminent domain, etc.
Third, probably public pressure, bad PR, maybe also try to yank their business license if they need one. If I was a liberal city, I could probably come up with goons to picket the place, boycotts, that sort of thing. Threaten tax audits, inspections, regulators, or whatever is applicable. For a church, yanking their non-profit status would work nicely.
Fourth, I'd grudgingly give up and let 'em build their stupid church. But being a petty city government, I'd engage in all sorts of petty BS to stick it too 'em. My citizens deserve a new sewer treatment plant, let's build one right next door (or a bomb screening center underground right below).
These are the standard real estate development hurdles that
everyone has to deal with in urban environments. Churches (whether Greek Orthodox or Muslim) are no different. They are not immune, 1A or not.
As relates to the mosque, the issue should have ended at the zoning board (i.e. zoning for the mosque should have been denied), but when it came time for the mayor to make that phone call, he sided in favor of the mosque instead of in favor of his city. Sadly, Bloomy doesn't have the same fortitude of his predecessor.