Yeah, I'm unsure if the South Park guys were being mean or just poking good-natured fun at Family Guy. Regardless, I agree with what was actually said about Family Guy, regardless of the sentiment behind it.

And they often use Cartman as a device to show that it's possible to do the right thing for the wrong reasons to point out the subtleties in many issues. They certainly weren't doing that here (as I don't think they were promoting not-depicting-Muhammad as the right thing to do), but there's more to their use of Cartman than there is to the character himself.