Potential cynic that I am, I have several residual thoughts on the issue.
Thought #1: I really want to believe what was in the apology letter sent to Shelly: it was a misunderstanding inadvertently caused by a junior member of the staff. I want to believe that had it been calmly brought to the attention of the Director of Publications by a single person (say, Shelley), that an apology letter would have been generated. But I'm having a hard time believing that. Perhaps I'm being unfair to Wiley and to the Society of Chemical Industry here, but I suspect that what really happened was that there was an eruption in the blogosphere, including from the high-profile blog BoingBoing, and lots of letters were generated. Wiley's response was, "OMG, what bad publicity! Retreat!" I know it's uncharitable to think that, but that is what I think.
Thought #2: at which point I start to feel sorry for this junior member of the staff who is being said to have made the mistake. Did she really make the mistake? Or was she implementing company policy, and is now being the designated fall-guy when things went south? I remember thinking the same things about private Lynndie England's high-profile case about torture at US-run prison Abu Ghraib; notice that no senior officers anywhere were charged.
Thought #3: but I also wonder what would have happened if Shelly wasn't here at scienceblogs.com, and if she didn't have a forum full of sympathetic, easily outraged bloggers who all like her. She posted that she was getting lawyergrams; we all got outraged. That was enough of a nucleation to send off things elsewhere into the blogosphere, including to the aforementioned BoingBoing. But the issues are larger than this one incident. This kind of copyright lawyergram, where some large interest asserts that it has more rights than it really does under the law, happens all the time. The small party usually has to put up and shut up, becuase they can't afford to defend themselves. Yay to the blogosphere for coming to Shelly's defense on this one, but let's not drop it and say "happy ending." The system is rotten, and Shelly may be one of the lucky ones for having people to defend her.
Thought #4: Boo to the blogosphere! Or not the blogosphere specifically, but to some individuals in the penumbra of the blogosphere who are a festering problem in cases like this. Notice this one excerpt from the apology letter sent to Shelly: "She has been most distressed by some abusive emails that she has received on this matter.".
Shelly's original call to action very clearly indicated that she was hoping people would send polite letters. Alas, the Great Unwashed on the Internet always include a large number who think that sending abusive letters will somehow help. I remember in the early 90's, when I was an Amiga fanatic, that computer columnists wouldn't take the Amiga community seriously. Why? Because if they wrote anything critical, they'd receive a huge number of letters, some of them highly immature and critical. The same thing happens with the Linux community now. The president of the AAS told us in a recent newsletter that part of the reason one of the higher-ups at NASA has a very poor view of astronomers in general is that he's been receiving some very abusive mails from astronomers.
Personal attack letters don't help, often are directed at the wrong target anyway, and only help to convince people that there is not a real viewpoint to be taken seriously, but that there are whining children who've been told that they can't have ice cream.