I wouldn't change preschools, as others have suggested, just to get more boys - assuming you are happy with everything else about the school. There's no reason to disrupt everything about him because of pressure to have him play more with his own gender.
What's interesting to me is that, at a church program of all places, kids are not being directed by parents to be more welcoming and open. That seems opposite to what any church's teachings are.
I think you just talk to him about being friends with people because of who they are and how they act, not what they are. If a certain group isn't playing nicely, it's not because they are girls - it's because they are THOSE girls.
I think there's a problem when we assign certain characteristics to toys - these toys are boy-toys, those over there are girl toys. There is a huge movement - with some stores responding - to de-genderize toys, stop with the pink and blue designations, and display toys by subject rather than by girl aisles and boy aisles. A lot of very brave little girls and their families stood up to the gender stereotyping (so they can have action figures and dinosaurs and Legos), and a lot of boys are going to benefit by getting the freedom to dress up in boas and tiaras. Manufacturers are changing packaging too, and catalogs are shifting the child models they use. There's also some movement in the clothing area, with character shirts for girls having more than princesses and unicorns.
So I'd say to keep encouraging him to play with kids he likes and with toys/activities that he enjoys, and help him through the rough patches where kids are already socialized to be exclusionary. It's about them and their pressures (from parents, TV and the toy industry), and not about anything wrong with him. So the girls at church shouldn't shun him, but he shouldn't be excluding an entire gender by saying he "only likes girls" - he just needs to meet some nicer and more flexible boys in the neighborhood or other activities (in terms of their play choices), and some less rigid girls at church.