Now in fairness, I've heard of this kind of thing before. Yes, I think it was an episode of Star Trek: The Next Generation, and it centered around how (fictional) Klingon culture holds the children accountable for the "sins" of the parents.
Yeah, I get it that this is a private school and they can choose to allow (or not allow) admission to anyone they want. But seriously, isn't it the child here that is being punished? The Catholic Church can certainly disagree with the lifestyle of the parents, and what's more, they can teach this disagreement to the students that attend their schools. This might in fact make things very uncomfortable for a child with two same-sex parents, and I'd wonder why they would want to attend such a school anyway. That aside though, what the Church is actually doing here is denying something to a child because of something that the child has absolutely no control over, namely the actions of parents.
Now let me ask this question: has the Church also denied admission to Catholic schools the children of reputed or convicted mobsters? Is engaging in murder, theft, graft, prostitution, etc. considered a "worse" sin than homosexuality in the eyes of the Church?
I could rag on about tolerance, but instead I'm going to leave this simple thought from Saint Augustine as my closing:
"Cum dilectione hominum et odio vitiorum"
...and I'm going to note here that the child in question is certainly NOT the sinner.