I certainly understand your question. It does help to understand it if we remember that that which is sin of those things that you listed (The Crusades per se cannot be construed as a sin) were done by individuals. The Church itself has not collapsed into a Culture of Death. It has stood against the Cathars, e.g., who did in fact propose a Culture of Death.
About the passage itself: It must be true that the passage must be interpreted somewhat differently than you have suggested. For example, the Lord said that He would never leave us or foresake us even unto the end of the age. He also said that the Holy Spirit it would lead us into all truth. If the gates of hell encroached upon the Church then these statements of Jesus would be untrue.
Moreover, the verb in this passage that you sited is Middle Voice. I.e., the passage might better be translated “The gates of hell will not be able to withstand the onslaught of the Church.” Surely, the death of Jesus Himself and the deaths of the millions of martyrs since might seem to indicate an encroachment by the powers of hell upon the kingdom of God. In reality these deaths constitute a victory of God over hell.
But, as you say, while these reflections help I certainly wish evil did not exist, anywhere. It’s existence forces me to my knees many times but then that is not an altogether bad thing. “How long, O Lord, will you allow the enemies of God’s people to kill our brothers and sisters. And the Lord gave them each a bright robe bleached bright in the blood of the Lamb thus mingling their blood with His and gave them a crown. He reassured them that it would not be long.”