In some ways, I find it more problematic to produce "The Sound of Music" at a public school than something like "Children of Eden." "Children of Eden" feels more mythic--SoM more personal and, in a strange way, mildly potentially proselytizing--though depicting the "faith journey" of Maria and the beliefs of the nuns seems pretty harmless. It does seem to me to assert that faith in a Christian god is a good thing, but so does "Everyman." And it certainly does not seem to me to argue that one faith is superior to another (and I am well aware of the irony inherent in characterizing a musical written by two Jewish men as "pro-Catholic").
I remember, in the 1960s, a classmate in my public elementary school bringing in the record "The Singing Nun," for Show and Tell, and the teacher nervously not being willing to let her play any of it for us. Yet, we did "The Sound of Music" as our Spring musical about eight years later. Maybe Broadway and R&H outweighed Debbie Reynolds in my town!