Aye... I'm almost afraid to say that we are Scouts. BUT, I had strong concerns and as a result, became a den leader so that I could quickly "out" if I saw anything like what the OP was concerned about. There are NO. OTHER. organizations in my area and sorry, but having just relocated (and moving 5 times in 18mo) I was so NOT in a place to start Earth Scouts (check them out, too, btw) or Spirals (which would've lined up with our beliefs a bit better). We tried 4-H but it was ALL. CRAFTS and usually with foods that my son couldn't eat (allergies) and they weren't exactly "for" trying to work with us.
This is one where I've set aside my issues with the organization as a whole for the benefits that come with the local chapter and the organization's program. FTR, I do NOT believe morals and ethics are confined to a specific faith and I think that agnostic and atheism are faiths like all others. I had the great fortune of moving from an area of the country that had a lot of "Sunday morning christians" and "religion" to a larger percentage that truly walked their talk. And while it may not be the same as my walk, I can respect them and they respect us. It's a nice microcosm.
I also occasionally go to Walmart because I truly need something that I cannot spend another dime on.
Call it what you will... but just for the OP's understanding of where MY opinion is coming from.
Our family intends to remain within the pack leadership as long as our son wants to remain a Scout so that if he is in ANY way going to be discriminated against, we are more likely to be in the know before it gets to him. There seems to be a contingent of people on the earth that have no tolerance for rambunctious or quirky boys and ours is both (sexual preference TBD as he is 7yo). And I'm hoping that if the day comes that we need to part ways for these reasons, he will be old enough to understand and process it with our guidance. In the meantime, he is learning a LOT and enjoying his time in Scouting.
I'm not saying the day won't come, but I'm not worried about it. And that's not because I'm "so sure it won't happen". It's because I know that it will be another learning experience for us to face together. Frankly, if it's going to affect him in Scouts, it's going to affect him elsewhere in life and we'll need the practice. If he got to Eagle, outted himself and couldn't be accepted, I don't find it much different than being politicked against for homecoming king or valedictorian in a public school (which, btw, totally happens... btdt).
Our pack meetings are held in the local public school and den meetings are round robin at people's houses. Since our pack is full of non-christian kids (the BSA has a faith emblem for Hindu, Islam, Buddhism... there are over a dozen and I can't remember them all) we don't generally have a PRAYER at a pack meeting, but we "give thanks" in a reverent and respectful way. The Cub Scout promise DOES reference a duty to God--which would not sit well with atheists. My family understands Father God and Mother Earth so for us, it's not really difficult to do this. But it would be hard for some. And while they recognize multiple faiths, they clearly don't UNDERSTAND some of them as they occasionally use "God" in their wording (I'm thinking of a Wolf requirement called "Duty to God" where the requirements are completely possible to complete as an agnostic or atheist if not for the word "God" in there--it's about your family's spiritual beliefs).
I'm also finding that the people where I live now--which includes a LOT of christians that are actually living christian lives in addition to a large Hindu population--have a really hard time wrapping their head around someone living with similar morals and ethics, but not having a defined faith. They simply have never seen it. It's not that they don't believe me, it just boggles their mind for lack of exposure. But similarly, the people where I'm from (where most "religious" people don't actually have faith or a clear spirituality) think that living here must make me nuts--because they've never seen people with true faith (which includes tolerance) and don't realize that it's easier to deal with people here because they're not complete hypocrites (which is what they're envisioning). They've seen the yappity-yaps that profess to be one thing and act like another.
It's been a surreal experience.