To me, this is not an issue whatsoever of free speech, but rather has everything to do with oppression and imperialism. Don't forget the power dynamic which is very prevalent here. That is why this is different than doing the same with, say, Christianity. The power dynamic that exists today between the east and the west, between the north and the south, between Christianity, Judaism and Islam, is what makes this wrong.
People are angry that their religion has been defiled, but the main point, is that people who are being targeted, killed, and oppressed directly via US and European imperialism have been pushed to the brink. It is akin to using political cartoons to satirize African-Americans during the periods of lynchings in the US. It is clearly another form of oppression - to ridicule those who we are killing by the tens of hundreds (thousands, even), and to desecrate what they consider to be sacred as yet another way of slowly killing.
I don't think the cartoons should ever have been published, not because of religion, but precisely because they are working to offend
an entire population of people who have been in the cross hairs of imperialism and brutality for years.