The biggest problem with the Crusades was that they were unsuccessful

Jonah Goldberg:

Banning ‘crusader’: A ludicrous new low in social justice

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... For most of last millennium, if you talked about the Crusades, you’d offend Christians. Why? Because the Christian West lost the Crusades, for the most part. Meanwhile, Muslims rarely talked about the Crusades, and if they did it was a matter of pride.

In the last century or two, the story of the Crusades was rewritten to fit an anti-imperial, anti-colonial, anti-capitalist narrative. The European invasion of the Middle East was the first chapter in the evil empire that was Western civilization.

This is all nonsense. Christianity — which is older than Islam — was in the Middle East far earlier (and Judaism has squatter’s rights going back millennia).
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Bernard Lewis, arguably the greatest living English-language historian of the Muslim world, writes: “The Crusades could more accurately be described as a limited, belated and, in the last analysis, ineffectual response to the jihad — a failed attempt to recover by a Christian holy war what had been lost to a Muslim holy war.”

Or, as historian Thomas Madden has written: “Now put this down in your notebook, because it will be on the test: The Crusades were in every way a defensive war. They were the West’s belated response to the Muslim conquest of fully two-thirds of the Christian world.”
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This reaction by a Catholic school makes no sense.  A school should take the opportunity to teach the facts rather than surrender to the prejudices of a hostile faith.