The Scouting experience will vary widely, depending on the leader and the group..my own time in the Boy Scouts (30 years ago) involved nothing that was overtly or forcibly religious, and certainly nothing that was paramilitary. Churches tend to be the hosts for Scout troops in my area, and I suppose some churches may be more involved than others.
Parenting and religious beliefs...whew, this can be a topic with a lot of contention. For me, growing up in the Methodist Church, the key factor was my parents. They were Christians, and we attended, but my parents were somewhat open-minded, and never tried to use fear to force a belief down my throat. This, to me, was a much bigger factor than the fact that I was in Boy Scouts, was baptized, went through Methodist Confirmation, etc. All of that happened to me, yet here I sit, years later, more Buddhist than anything else.
Long story short...I'm not sure I'd worry so much about a tiny bit of God indoctrination. If the parenting is done correctly, without fear and hate, and with good example, the kid will find the path that suits them...and that's the goal, right? Not to make little clones of ourselves. Where ever you move, there will be someone around that wants to convince them that their belief system is the best one. Just make sure that the kid has the intellectual tools and open mind to figure things out.
This is how I'm raising my 2 daughters. My eldest is now to the point where I think she'd detect when we're trying to hold her back from something...and that might intrigue her with it all the more. She's a bright kid..certainly smarter than her old man.