He can apologize to the Crusades for the outcome of the First Crusade by saying "I apologize that some Christians, of their own free will, became overzealous in their pursuit of a good cause, not because it was the fault of the Church, but merely to humor you." That will only occur after their imams, mullahs, and ayatollahs apologize to the Roman Catholic, Coptic, and Eastern Orthodox Chruches for the entire Islamic conquest from the Battle of Yarmouk to the Battle of Tours.
Meanwhile, the pope can also apologize the Greek Christians for the Fourth Crusade by saying "I guess excommunicating them twice just wasn't enough!"
He can apologize for the Crusades right after every imam apologizes for what made them necessary in the first place.