Churches are parts of their community. Moving them isn't always an option. In NYC the Catholic churches are particularly tied to their neighborhoods, historically, so there really aren't many places to move to and still provide a place for that same community.
The church could have been established as floors 2 through 10 (or indeed, floors 70 through 80) of a conventional rectangular box skyscraper, instead of building what is effectively a large shack at ground level, and designing a risky skyscraper without corner supports because one of those corners would pierce the shack.
And when the poor and homeless show up looking for the soup kitchen and temporary shelter? That should fly real well with the monied gentry on the 50th floor.