What Pope Frank said is here.
There's a subtle normative/descriptive distinction at work here. Frank was almost surely making a descriptive statement about punching someone, not a normative one. What he would (probably) do, not what he should do. He clearly wasn't saying the killers should have done what they did but he may or may not have been leveraging the ambiguity between normative and descriptive to suggest that the victims kinda deserved it. Your call. I don't happen to think so. But the gist of the statement is the descriptive "if X, then Y."
Just-world fallacy enthusiasts will say if Y, then whatever X was (the cause) was something you shouldn't have done (you deserved it). If he's implying the just-world fallacy, this is apologetics for the killers. I really doubt that he is.
Logically, though, "I would punch someone who..." (descriptive: it's just what would happen) is not necessarily an endorsement (normative: it's what should happen) of "punching someone who..." Assume so, and run into the tu quoque. Personally, there are plenty of things I do that I don't endorse. If a lung specialist smokes, it doesn't make smoking a healthy activity, etc.
As for the "don't be offensive" bit, it's nice for a rationalist to say "nothing offends me" (some do) but it's never quite true. It's a nice goal (normative), but not an accurate description of any real person. Self-censorship is an indispensable ingredient in social interactions. It's probably best to be as unoffendable as possible (and willing to give up beliefs shown to be crappy) but intentionally causing offense is a case by case matter. I generally wish more people would be less self-censoring, but I also try not to say racist and misogynist things. People with stupid ideas should stop having/saying/drawing them, and that includes racist French magazines. Doesn't mean it should be illegal, doesn't mean the bad idea people should die, but I would like harmful ideas to stop reproducing.
In the end, this is politics. Mockery of Islam serves power because it's the enemy du jour. If I were living in Nazi Germany, I'd be very careful even making accurate criticisms of Judaism, let alone caricatures aimed at a racialized underclass (Islam isn't a race, but Black isn't either -- there are no races, just outgroups categorized for ingroup convenience). Criticism of the enemy will get co-signed immediately, whereas criticisms of the ingroup will be condemned.
If you're talking face to face with a devout Muslim, telling them how absurd their version of monotheism is is fair game. Rationality over hurt feelings. But feeding hate of an already dehumanized group is a political issue. Mockery that punches down has real social-political consequences apart from hurt feelings. Drone bombings, social and economic opportunities...
There's the critique of bad traditional religious ideas (why is your god so genocidal?) and there's the critique of state power today. The one will use the other. The one that's important, today, will use criticisms of the one that's not, today, to its advantage, just as those did when they could, back when.