I've got a couple of questions about this.
I haven't read the complete transcript of what the Pope said, but as I understand it, he read from a centuries-old manuscript from a Pope who, apparently during the time of the Crusades, characterized the Muslims as evil and made several nasty comments about their religion in general.
My first question is, why bring the subject up at all? If he wanted to make the point that religiions should not be at war, literally, with those who do not espouse their views, I'm sure he could have found a better way to make that point than to use an old text from a time when not only the Muslim religion, but Catholicism itself was intolerant of other religions.
Second, though there are historical reasons behind the text, and the point of view it espoused, if the current Pope was going to use it as some sort of example, would it not have made sense for him to explain then, at the time he made the comments and used the text, that the view of the Muslim religion presented by the text did not reflect his or the current Catholic church's view of the Muslim religion?
Seems to me the Pope fucked up. He could have brought up the issue of radical elements of [any religion] going to war with those who did not share their views, without doing it in a manner that gave the impression he, and the Catholic church, shared the views given in some ancient text written by a Pope who has been dead hundreds of years.