Generally speaking I don't find historical ironies like this offensive, but this one comes pretty close. Let's just say if a Jihadi wonder were added I would be equally queasy about it.
I mean the Inquisition is in only one scenario. Christians could only get so worked up about the ToE: no one practices that religion anymore. Every Japanese will tell you that as bad as the nukes were, many more civilians died to ordinary bombs. Ultimately the war itself was the trauma and the nuke just a punctuation mark at the end. I can't think of too many fellow atheists who would be offended by the presence of religious advances and wonders in the game. It's hard to imagine the march of human history without all those colorful myths and faerie tales; they are a legitimate part of our collective cultural heritage even if they're factually wrong. It's not like I'm going to insist that Shakespear be removed from the game just because his plays were fiction.
So while there are other things you could compare to the crusaders, but the crusaders are right on the edge of what I consider acceptable, as would be the case if someone made a Dachau city improvement or a Witch Trials wonder.
crusader is not a generic term, it is derived from the word crusade which is derived from the Latin word crux, meaning cross. the word crusade refers to the march of warriors and peasants throughout Europe to Muslim lands in the 11th, 12th and 13th centuries, with papal sanction.
Yes, like all words "crusade" has a specific origin, but like most words it has evolved over time and picked up new meanings.
We Americans are notoriously poor at history, so most of us think of "crusades" purely in its modern meanings and not in its original meaning. I've even heard Arab Americans causually use the term in conversations (with the modern meaning of course).
As for said modern usage, it is interesting that the new meaning is something of a double-edged sword. It can be either a comliment or insult, but often it implies both. On the one hand it means a person is strongly motivated or motivated by morality, but it also implies that the person is a dangerous fanatic, possibly immune to reason.
A good example would be Ralph Nader. Throughout his public life both his friends and enemies have used the word "crusader" to describe him.
Historical Qubble:
Both the Crusades and the Inquisition killed both Jews and Muslims. It is incorrect to associate one with Jews and the other with Muslims.