You're saying there was a time when the Scouts allowed open homosexuals, or atheists, as leaders -- sometime before "the unde influence of the Mormon Church" started? I say you're full of it.
As for whether they should get public benefits - - if other private organizations are allowed public benefits, the scouts can't be discriminated against merely because they have beliefs you don't agree with. Right. let's have government start discriminating against every organization that doesn't buy into your PC worldview.