Tolerance does NOT equal acceptance. I "tolerate" being around athiests - I sit beside them, I talk with them, I eat with them, I treat them like every other decent human being. That doesn't mean I accept their belief. As such, a group doesn't need to accept members that fall outside of its beliefs - but it can teach tolerance (be nice to "those other people" instead of kicking the shit out of them).

The Boys Scouts have a committee that determines whether or not a group is appropriate. Likely this matter will get bumped up to them and in a few weeks/months/years we'll get an official stance on Boy Scouts and Wiccans.

You're right, this does suck for the kids. But it's not their fault - it's their parents. THEY should have been the ones smart enough to see the problem here.