What is it that defines this as discrimination?
I always thought of "discrimination" as treating someone differently just because you didn't like something about them or that was different about them. There are more technical and legal definitions, but to me "discrimination" could be as much about race or sexual orientation as it could be country folk vs city folk or any other nebulous "us" vs "them" designation you'd care to make up (Star Wars vs Star Trek fans, maybe).
If you change the names a little, if an all Caucasian school kicks out two African American kids for being African American, there would be riots outside the school. Or, to use my original example, if the school kicked out two kids because they owned guns and belonged to the NRA (which go against their religion), we'd be saying every bad thing about the school we can think of.
Now personally, I can't imagine why a lesbian couple, who will be told by the school that they are going to hell for their ways, would want to go to that school. But that's not the point. Heck, I grew up in 12 years of Catholic education, and we were pretty much all convinced that we were all going to hell no matter what we did or didn't do. But that's STILL not the point. Fifty years ago, it was acceptable to intentionally break kids into separate schools because of their skin color. Today it's not. Any time you treat someone differently just for being different (not for violating some pre-set, defensible rule), I'd call that discrimination.
The court is now giving that school the ability to do anything it wants if someone doesn't comply with their "Christian principles". You'd better hope none of their parents get divorced or that none of the students miss church one week, or they could be the next ones to be expelled.
I get really touchy about groups being given special privileges to do whatever they want because "my religion says so." With so many religions out there, it's going to eventually let someone somewhere have an exception to do almost anything: kill, maim, rape... hey, why not? Because we didn't draw a line early on with discrimination.