This is an important part of the Faith that they are learning in these classes. So, if the parents are rarely showing up for Mass, it doesn't really help reinforce what the kids are learning.
That said, I'm not in a position to say whether or not this pastor made the right call.
It's simple ..
If a pastor wants' to make a statement against parents that are not setting a good catholic example, they should treat them just as they treat non-catholic parents. i.e. don't give them the 'catholic student' school rates.
To 'punish' or 'disallow' class attendence, graduation, sacramental receipt for anyone (regardless of their parents faith) shows a real 'hollowness' of the faith that is being preached at this particular church and not a proper Christian message that makes salvation available for all.
And yes, the MSM may be getting this whole thing wrong so I am only commenting on the article as presented.