how hard would it honestly be to tell schools they are no longer allowed to teach religion, hold mass, and hang dead Jesus on the walls of every class?

It wouldn't be hard at all, but that's not the reality of merging both school boards.

You can literally change that over night, it doesn't stop the fact that a school has a massive cross shaped window in one of the walls and is called "St Michael the Archangel". It doesn't stop the fact that two custodians who work across the street from each other have different benefits, salaries, and unions, all while working for the same entity. It doesn't stop that each board has their own community voted representatives which have a say in things like school budgets and projects.

Case in point, where I grew up in northern Ontario, the French Catholic highschool only had 3-4 students per class, separate busses, etc...

You're looking at this at such a low level narrow sighted level. Yeah man, it's not complicated to come to the conclusion that a school with <100 students gets shutdown.