It doesn't matter who the Pope was talking to. The pope said more than just that little bit from the 14th Century Byzantine Emporer. He gave a good speech with a good summary. Are we no longer allowed to tell things like they are while providing historical evidence to support our summaries anymore? The violent ways of the Muslim have been ongoing since Mohammed's time. The Catholic and Christian churches stopped behaving that way quite a while ago. When was the last Holy War declared by Rome again? When did the Spanish Inquisition occur? When did the Spaniards come to America and commit their sins in the name of the church? Was WWII and WWI christian religious wars declared by the heads of the christian churches? How about the troubles today, does anyone really believe the Christian and Jews have declared holy war on the Muslim, or do people think that it's more of a retaliation thing for abuses which Muslims have done?
No, I don't believe it hiding history and distorting facts just because someone out there might find it offensive. If you don't want to be known as a hooker then you don't go and solicit johns. If you don't want to be known as a thief, then you don't steal. If you don't want to be known as a violent religion then you do not commit violence in the name of that religion. This is pretty simple stuff.