2) Email the Biology-online editor and attempt to reach him by phone, and ask whether he in fact sent the email in question
Had the answer to point #2 been "yes", then Dr. Lee's blog post should have remained intact, and the next issue would be, what to do about SciAm's now troubled relationship with Biology-online.
Apparently the editor-in-chief did none of those things. After all, it was "Friday before a long weekend." Everyone has things to do... places to go... people to meet.
Actually, they apparently did pretty much do that. When they didn't get a response back, they went ahead and reposted the original blog post. I'm a bit surprised. I would have thought that a manager would want to deal with the other person's manager quietly. That's just the way they usually want to handle things. Who's turf is who's is very important to managers. Normally, it would probably better to let the management of Biology Online have a crack at dealing with the problem first, and to apply pressure only if the results weren't satisfactory.
BTW, the guy who sent the email was fired, so there isn't a "troubled relationship" with Biology Online to deal with.
Regarding the first thing you think the Editor In Chief should have done, I'm not sure any verification from Dr. Lee was necessary, but I do think that Dr. Lee should have been notified as soon as the blog post was pulled and given an explanation. Dr. Lee would have been a lot less upset if she had just been told, "That email is clearly not acceptable. Let me handle it." Of course, the Editor In Chief had better handle it then.