There are still non-mormon controlled troops around. My son was cub leader for his son in the bay area. No religious interference in his area.
I made Eagle, and I dont remember any Mormons even being in the troops in my area, let alone controlling them. I also hiked Philmont the summer of 99 and I dont remember anything mentioning Mormons.
The event in the article seems to be only a special one for Mormon scouts.