Well, PZ Myers has not lost his job over this mess, but someone else has. Melanie Kroll, an employee of 1800Flowers, was fired for sending him a death threat with her work email. Turns out, it was actually her husband who sent the abhorrent email, but since it was her work account, she was responsible for its misuse.
In other news, Nick Milne has perhaps the best and most comprehensive discussion of the the whole series of events, from the incident at the University of Central Florida up to the present (HT: Matteo). In particular, he includes much more about what the student in question actually did, which places him in a much worse light than it had seemed at first (though I can't say it justifies Bill Donohue's making a national issue out of it). If you've been following this story at all, you'll definitely want to check out Milne's even-handed post.
UPDATE: Mark Shea, of Catholic and Enjoying It, has added his own lengthy response. I'm not in complete agreement with the post, but his conclusion is spot on:
It is right and just to be angered by Myers' assault on the Eucharist. Not all anger is sinful. But the purpose of anger is action, not desire for vengeance. Catholics who threaten violence against Myers in return disgrace our Lord who forgave his murderers and, just as surely, extends forgiveness to Myers even as he fights him with the same goads with which he fought Saul of Tarsus. Our task is to realize that our principal audience is not Myers and his vicious crew, but all the onlookers in our culture, who want to know if there is any real difference between Catholics and Myers. Show them, by your actions, that there is. The world is watching.