We are one of the ones that did Boy Scouts because locally it was OK from a non-discrimination standpoint.

Earth Scouts is another option: http://earthcharterus.org/programs/earth-scouts-and-parenting/

4-H is a well-established alternative, if you don't want to go with a startup org.

Campfire in Davis seemed to be more Scout-ish than Y-ish, so it may depend on the individual group/area.

Frontier Girls looks interesting for girls. We're considering that because I'm not hearing particularly good things about the direction GS is taking (even from a liberal perspective).