I included religious activities in my application last year. I am a devout Christian, and I'm very unlikely to stop being one in the coming years. My faith influences my decisions including the one to being a physician. If I left out "religious things" on my app, there would have been gaping holes in my app. I think stuff like ethnicity, sexual orientation and religious affiliations is about presentation. Being a christian put me in contact with people I could have never met (missionary trips etc), increased my awareness of social situations and increased my ability to be a passive observer when necessary (ie observing and learning before judging/ giving my opinion). I think those things will make me a better physician. Your pastor is in a perfect situation to give you a wonderful recommendation. Have your Pastor emphasize how your religious conviction has helped you "outside" the church. I think you should also make sure you get letters from "academic people". Don't write all of your essays from a religious point of view or based on your religious experience. I think as long as you're not using your religion as a cover for hatred, a LOR from your Pastor will be fine