So what exactly is the problem? 
Is it that Catholics are not a minority?
Is it that non-Catholics are attending Catholic schools?
Is it that Catholic schools get provincial funding and other non-Catholic private schools don't?
This article doesn't do a very good job of explaining what is really going on.
Once the notwithstanding clause is used the floodgates will open around the country.
An explanation of which parts of the charter cannot be overridden by the clause would have made the article more useful too.