One aspect of the cracker controversy that seems to have escaped some critics is the fundamental motivation of critics such as PZ Myers (and myself) and what specifically we're reacting to.
This controversy did not arise because atheists don't like religion.
This controversy did not arise because atheists think communion and transubstantiation are ridiculous.
Many of us (myself included) don't like religion, and many of us think communion and transubstantiation are ridiculous. But that's not what this whole issue is about.
Nobody ever said, "I can't stand Catholics because they have a dumb religion, let's go desecrate their wafers." Nobody ever said, "Let's show the world how ridiculous Catholic communion is."
This controversy arose because of Catholics' insane overreaction to what was at worst a harmless, albeit juvenile, prank and at best nothing more than simple curiosity.
This overreaction is many orders of magnitude more serious than even the most uncharitable interpretation of the original offense. Regardless of how one feels about desecrating communion wafers, civilized, rational human beings cannot permit such an overreaction to an action that caused no actual harm to anyone. Even worse, many many Catholics — including official and prestigious advocates — are defending the overreaction by virtue of the fervency and the religious character of their beliefs. Again, civilized, rational human beings cannot allow this sort of justification to stand.
If the original prank were not about specifically religious belief, those overreacting would be universally condemned. If someone were receiving death threats and feared physical violence because he "desecrated" an apple pie, there would be no controversy at all. Everyone would consider those issuing the death threats to be complete lunatics. It's retarded to permit Catholics an exception to this standard because their beliefs are irrational and their fervency extreme.
We can and should apply normal legal consequences to those who break the law by harming, assaulting and threatening people. But more is required.
We cannot apply legal punishment (much as we might like to) to stupidity and assholiness, so the best way to counter the Catholics' ridiculous overreaction is with widespread public ridicule and humiliation. Any activity, any response that harms no one, threatens no one with actual harm, but highlights the stupidity of making death threats and threats of violence over "harm" to a cracker is not only permissible, but almost obligatory to anyone with an interest in maintaining standards of rational civility.