Man, I'd say that the desire amongst certain christians to paint all atheists with the same brush is quite similar to your desire to paint all christians with the same brush.
What you're saying, essentially, is a private group, that exists mainly to the purpose of teaching kids morality, is wrong because they exclude those who unrepentently do what they perceive to be immoral. Am I correct?
When it comes down to it, I agree. I think it's wrong that they discriminate against homosexuals and atheists. But that is because I believe different things to be moral than they do.
You said, "Standing up for what you feel is right is commendable, but not if you're standing on others in the process". It would be nice if everything that was right didn't hurt anyone, but this world is far too complex. If you're standing up for something, you're standing up against something. And if you're standing up against something, you're inevitably standing up against someone.
Inevitably, if you admit that there is such a thing as morality, then you have to admit that there will be people who will be doing things that are immoral. Since morality is among people very subjective, there will be differences of opinion on who is doing something immoral, and thus if we allow ourselves caught up in the subjectivity, there is no objective way to determine who's discriminating, and who's standing up for what they think is right.
For example, say you started a group that was intended to teach morality to children. Would you be at all discriminatory against people of different beliefs on morality? If a kid grew up, went through your program, did everything, and if not for some belief, possibly that all atheists are heathens and must be converted, he would reach some position of authority, would you still put him in this position of authority?
I'd assume not, just as much as I probably wouldn't put someone sharing your lack of respect for people of faith in a position of authority.
In any moral question, some people think the practice is ok, and others don't. To the people who find the practice ok, excluding those who do this practice may seem like discrimination, while to those who do not think it's ok, it may seem that the group is merely standing up for what's right.
And it's hypocritical to call for people to be tolerant of your morals being different from theirs while you are not tolerant of theirs being different from yours.