Unfortunately 90%(at a guess) of the country want their kids to have a religious education. Someday they'll get it sorted.
I would seriously raise my eye-brows at 90%, don't think that's anywhere near the truth
I went to a religious secondary school, runs by Nuns it was, and it was mostly grand, but occasionaly it was a total pain in the hole and fustrating and unfair and stupid (as most things are too a teen!) But I was lucky in so far as my parents would always say "yeah Sr Anne is pretty mental" take my side on arguments "yeah we don't think Queen are satanic either", never freaked out, "we don't think you should bury your Dungeons and Dragons books like your R.E. teacher said" or simply explain that sometimes nutty people are running the show and you just have to tell with it.
In fact that may be the only thing that school thought me
Anyhow at the end of the day it would be nice to send a kid to a school with a moral ethos you agree with. But if he does end up going down the road to the local Saint Aloisius or whatever I'm sure he'll be clued in enough to sort the bullshit and you seem smart enough and concerned enough to keep him on the straight and narrow.