Alislam.org: An English translation of a sermon by Hadhrat Khalifatul Masih V aba September 15, 2006
It was in the news yesterday that during a lecture at a university in Germany, the Pope spoke with reference to another writer about certain Islamic teachings, the Holy Qur’an and the Holy Prophet (peace and blessings of Allah be on him) which do not have the remotest connection with Islam. 
This is their way to most cleverly speak with reference to another person, thus trying to save their own skin yet putting across what they wish to say. The Pope has tried to create a false impression about the Holy Qur’an, Islam and the founder of Islam (peace and blessings of Allah be on him) by saying certain things. While this must have created disquiet among the Muslims it also demonstrates their own inner feelings against Islam. Such is the stature of the Pope that no matter with what reference he spoke, it was not appropriate for him to have made these observations. In the current climate when in the world, in the West, hatred against the Muslims is being generated through one reference or the other. For the Pope to have stated such a matter is akin to inflaming the situation. More:
This is their way to most cleverly speak with reference to another person, thus trying to save their own skin yet putting across what they wish to say. The Pope has tried to create a false impression about the Holy Qur’an, Islam and the founder of Islam (peace and blessings of Allah be on him) by saying certain things. While this must have created disquiet among the Muslims it also demonstrates their own inner feelings against Islam. Such is the stature of the Pope that no matter with what reference he spoke, it was not appropriate for him to have made these observations. In the current climate when in the world, in the West, hatred against the Muslims is being generated through one reference or the other. For the Pope to have stated such a matter is akin to inflaming the situation. More:
Yes, the Pope had uttered some bad words against Islam with reference to some other person. That was to avoid his own involvement. That was not good.
If he had said such a thing, he should have given his own remarks in favor or against it. He should have denied any support to those bad remarks. But he did not do that. Pope got a good reply from the Khalifah sahib of the promised Masiha a.s. That was a befitting reply.