Hello, and thanks for expressing it so well, from a parent whose kids are involved in the Boy Scouts precisely for the values that the Boy Scouts hold, and who really does not give two sh!ts about some atheist's "intellectual and spiritual journey."
This 19-yr-old has a chance to make his separation from the Boy Scouts into a valuable experience by which he can clarify to himself what he truly believes (or doesn't believe), and who he truly is.
Instead, he has chosen to join the legion of whining malcontents who never cease in their efforts to suppress legitimate expression of beliefs by those whom they don't agree with. Or he is being used by said legion of whining malcontents.
In my opinion, atheism or anti-theism, viewed practically, results in a worship of one's Self. Let 'em worship their Selves. I'm not stopping them, nor am I joining organizations filled with atheists and trying to impose MY belief in God upon THEM.
Similarly, I do not go to homosexual organizations, pass myself off as one who is interested in their activities, and then try to raise dissent within the organization. Let them have their unity and their organizations. As many posters here know, there was at least one homosexual organization which backed the Boy Scouts' earlier stance on not having homosexual leaders. This homosexual organization submitted a Friend of the Court brief in support of the Boy Scouts. They had enough sense to realize that there was an issue bigger than the Boy Scouts or homosexuality at stake--freedom of association.