From a resale stand point I wouldn't. I am not a Realtor only an appraiser but it might have to be disclosed to every potential buyer of that property that it was once a church.
There is no might, he would have to disclose that it was a church, and I would think that might scare off many.
I had a very good friend that converted a 10,000+ Sqft train station into a house, and I have seen old school houses renovate. The main thing is getting it for the right price to make it worth the trouble, and I do mean trouble.
Even if it has great bones, you will need to bring in an architect, and have plans drawn up for the city, and possibly even the county to ok the project. The electrical, plumbing, interior framing and A/C would cost just about as much as building a new home, so unless you really like the location, and get it for a great price, I don't see how it would be worth the money.
Just my $0.02