The Muslim overreaction to the pope's remarks may go to support his point about Muslim's problems with rationality.
Had Pope Benedict XVI omitted the citation of Emperor Manuel II Paleologus's remarks about Prophet Muhammad bringing only what is "evil and inhuman" to the world, a quote he himself admits was "marginal" to his argument, then he would have focused attention on his real offence in that scholarly talk: his shoddy scholarship on Islam.
He would have also permitted a more healthy focus on his central argument, that modern secular rationalism needs to heed the contribution of faith to enable it to break out of the narrow confines of positivism and empiricism.
The skeleton of the pope's argument can be summed up in the following syllogism: Islam is faith devoid of reason; modern secularism is reason devoid of faith; Christianity is a dynamic wedding of faith to reason.
http://english.aljazeera.net/NR/exeres/912E1DED-250C-4956-8A50-8D3FCDB90E6F.htm