I usually point out the conversation Ray and Winston had in the Ecto-1 like noted already. I also point to the archbishop part as well in the movie.
What conclusion I get is religion doesn't really get explained in the movie, but is noted that the writers did seem to suggest that religion should not see the ghostbusters as a threat. They are the good guys. While god may or may not agree with the people that are the ghostbusters, the overall mission at least in the first movie was to take out a false god named Gozer.
Ok thats all I know. lol