I'm more agnostic than I am anything. Do I believe there's something bigger than me out there? Probably. Do I have any idea what the fuck it is? No clue, but I figure they just wants us to all be good to each other. So as long as you're doing that, I figure you're good.
I came from a mixed faith household. Mom's Catholic, Dad's Jewish. And whenever I do go to services with them, which is mostly just for important holidays, neither her church or his temple ever treat me that way. They're just... always happy to see me and ask how I've been since the last time I visited.
If yours is going to treat you like that, I think it's time to find somewhere new to go. Or just start the HolyChurch of Pajamas.