Don't soften this. Christians did terrible things in those centuries. The right Christian response is repentance, not deflection. But the popular narrative is also significantly distorted.
The Crusades — what's true
The First Crusade (1099) ended with a massacre in Jerusalem that horrifies any honest reader. The Fourth Crusade (1204) sacked Constantinople — Christians butchering Christians — a wound the Orthodox East has not forgotten. Pope John Paul II formally apologized in 2001. Patriarch Bartholomew accepted the apology.
What gets left out
The Crusades were called after nearly 400 years of Islamic conquest of formerly Christian lands (Syria, Egypt, North Africa, Spain, Asia Minor). The initial call was a defensive response to the request of the Eastern Emperor for help against Seljuk advances. None of that excuses the atrocities — but the "peaceful Christendom suddenly attacked Islam" framing is historically false (see Rodney Stark, Bernard Lewis).
The Inquisition — what's true
The Spanish Inquisition (1478–1834) executed roughly 3,000–5,000 people over 350 years, according to modern historians who have actually read the archives (Henry Kamen, Edward Peters). That is 3,000 too many. It is not the millions of popular legend, and it is not the worst killer in early modern Europe (state torture and witch trials in Protestant lands were often worse per capita).
What the Orthodox East did not do
There was no Orthodox Crusade or Inquisition. Orthodox lands spent most of those centuries under Islamic rule (1453–1820s for the Greeks; 240+ years for the Russians under the Mongols). The Orthodox memory of these centuries is one of martyrdom, not conquest.
The Orthodox lens
The Christ we follow refused the sword. "Put your sword back in its place" (Matt. 26:52). Whenever Christians have taken up the sword for Christ, we have betrayed him — and the Church must say so plainly.
A pastoral word
If you have been wounded by Christians' violence — or by their hypocrisy in claiming Christ while wielding it — bring that wound to Christ himself, not to his unfaithful followers. He bled at the hands of religious men too. He understands.