I couldn't understand what the big deal was. We had Christians and Jews who were raised side by side from Tiger Cubs back in Boca Raton and my son loved his friends regardless of how they worship our common God. Those folks were just wonderful and provided years of outstanding childhood experiences for my son.
What was it about the Mormons that they would not accept a Christian?
This was a hard experience for me, and it has left me very suspicious as to the intent to segregate Mormons and non-Mormons under the name of "Scouting". We had never run into any sort of religious segregation before.
Frankly, it has turned me off to whatever Mormon scouting represents. It certainly is not an effort to reach out to the community "outsiders" are clearly not welcome.
With the Mormon's missionary focus, it really seems odd that someone would behave that way.
There are many LDS Scouting units that have non-LDS members. However, LDS Scouting is a different program than traditional Boy Scouts of America Scouting. The LDS Church was the first institutional sponsor of Boy Scouting. Under the terms of its 1913 agreement with the Boy Scouts of America and subsequent agreements, the LDS Church is permitted to make changes to the traditional Scouting program.
Here's a copy of the LDS "Green Book" (although not the current version, because I don't have a current link) on LDS Scouting. You'll see that the purpose of Scouting is to supplement the purposes of Aaronic Priesthood quorums and LDS Primary classes. Youth leaders are selected by the bishopric, not the youth. The responsibility for training adult Scouters falls upon the bishopric, not the BSA. Traditional Boy Scouting is designed to exist only until the youth are fourteen (not eighteen), and at fifteen, the youth move into Varsity Scouting (a national program, but it exists almost exclusively for the purposes of LDS Scouting). There is significantly less camping experience in LDS Scouting
I'm a former Council Commissioner of one of the nation's largest BSA Councils, and I work in national and regional roles.
It's simply a different program. Although there are special relationships for some groups, such as Catholic Scouting, nothing comes close to the fact that the BSA maintains a separate LDS-BSA relationship.
I could discuss the issue at length. There are excellent LDS Scout units. There are excellent LDS Scout leaders. LDS Scouting is simply a different program than traditional BSA Scouting.
Mormon scouting is used to train their younger boys as they enter the Aaronic priesthood. If they would have allowed your son in, he probably wouldn't be allowed to be a leader since only those in the priesthood were allowed. This is particuarly evident before 1978 when lds troops refused to allow black boys leadership positions because the mormon church policy was that blacks couldn't be appointed into any priesthood.
Hope you found a better troop. If not, look up the nearest Royal Ranger Outpost - very similar in organization and activities and they will have no problem accepting your son into the outpost.