I think that article lost a bit of nuance somewhere. The Pope was specifically defending the right of Muslims to protest peacefully against deliberate insults to their religion:
> Francis spoke about the Paris attacks while on his way to the Philippines, where around 1,500 Muslims protested yesterday against the depictions of the Prophet in the satirical French magazine Charlie Hebdo. [0]
He also explicitly condemned violence:
> Francis insisted that it was an “aberration” to kill in the name of God and said religion can never be used to justify violence. [0]
So, he wasn't justifying the attack on the Charlie Hebdo office.
Such an attitude is abhorrent and shameful.