is that you need to separate the nonsense national wraps itself around and look at it unit by unit. The way the program is carried out is what matters, and the troop is where the program is carried out.
I've seen troops from churches adhere strictly to common belief systems. I've seen secular troops with liberal leaders. The program itself is pretty liberal when you look at it--especially in being stewards of nature.
I can tell you a couple of stories from a Council perspective as well:
1> I am a Wood Badge trained adult leader. That's kind of a big deal for what it's worth. A couple of months after our pre-course was finished, we met for a reunion. A woman there brought her partner (who had already completed the full course with her Wood Badge training troop previously.) The situation was not paraded, but was obvious enough, No one said a word.
2> I went to summer camp 4-5 times in the past 8 years. Every year, adult representatives from each troop gather to listen to whatever the Chief Scout Executive wants to present. It's usually about recruiting, or major facilities being planned or whatever. Every year though, we always got the dubious rationalization of the anti-gay, anti-atheist policies. In my experience, no one gave a shit. Sex, heterosexual or homosexual, was not a reasonable discussion to have while carrying out the program.
No one ever questioned my sexuality (I happen to be straight) or my religion (many would consider me an atheist). It just doesn't come up in a meaningful way.
My point to all of this is that their policies of exclusion are largely unenforceable. That's a good thing, because it's a good program. National needs to quit being a puppet of the LDS--no mistake about it. They deserve all of the criticism they get. This should be somewhat amusing to see how they react to the news.