I know you're asking a rhetorical question, but it's a good one.
What parents would send their kids to such an organization?
The answer is that there are some who would. Those parents so steeped in the concept of diversity and multiculturism that they support their kids joining Gay Lib groups and participating in a "Day of Silence" at school to show soladairity with the homosexuals of the world...
If Scouts were to have active homosexual leadership, (I mean out in the open leaders who openly discuss their sex lives with the troop, (yuk) Then this troop would see membership, support, and charter decline as well as the national leadership pulling the troop's official charter.
As for athiests, the Scouts are pretty loose about what constitutes a "Duty to G-d" and they allow a scout to define his belief in "any higher power" which can include the collective laws of nature as well as all major religions dieties.