Well it's kind of a trap.
You can relieve any garrison under seige which will not go against your reputation, but you cannot take one of their cities while the ban is in effect. This may seem bad on the face of it but the best thing to do is lift any of your own seiges and just stand or back up to the edge of your territory.

When you get attacked, they may get excommunicated or not depending on their standing with the Pope.

The very first thing I do as any Catholic nation is make a beeline to Rome with a diplomat. His sole purpose is to give the Pope florins and try to enter alliance etc with him. Anything at all to get the Popometer up. This also allows me the oppurtunity to chose the Crusade target . Generally, I pick a region that is closer than the Holy Land if I am playing as England.

That way when those factions attack me, then they take the rep hit more than I do.

It does require some discipline, but revenge is a dish best served cold.