My position hasn't yet crystallized, but it seems to me that when school is out, the school building ceases to be a school and becomes just a building -- a public building available for public use. As such, I wouldn't object to either the BSA or atheists using it, just as I wouldn't object to them using a public park or public roads.
The BSA's recruiting during school hours in a public school does seem inappropriate to me, even though I think the BSA's activities are beneficial for boys and the community at large. But of course that's the problem with public schools: they make something that is morally right (the teaching of religious morality) into something that is morally wrong (the teaching of religious morality using someone else's money).
I think that public schools and buildings, even off-hours, are another matter because the buildings themselves are intended for gov't activities alone (public education, and so on). Thus, a political or religious group practicing there would constitute a violation of the First Amendment.