My scout troop was pretty mainstream and "cool" because nobody went in there and expected the troop to change just to fit their particular hangups.
Personally, I just inserted the word "my" in front of "God", and that was good enough for me. Nobody ever suspected that My God could have been a beer for all they knew, and I had a great time in the scouts.
Hard Core athiests are just as crazy as religious whackos, and IMHO neither of them need to be running scout troops. The more people get involved and simply insist on the scouts teaching a moral code of behavior, the better, because that can mean different things for each person and isn't tied to any particular religion, faith, or faith of disbelief.
And if anyone doesn't like it, they're perfectly free to start their own group. Freedom doesn't mean the right to force groups to cater to your own personal hangups.