I'm an Eagle Scout and an atheist.
Where I came from, each troop did as they wanted. If the council/district wanted us to do something we didn't agree with, we said F*ck Them.
We didn't give a darn what sexual orientation or religion(or lack of) you were.
The only person we ever had to kick out of our troop was a Bipolar kid who had attacked others for no reason and was a threat to himself.
There are a lot of pansy scouts and troops out there that I would rather do without, but with the good, there must be the bad.