Open sourcing something doesn't necessarily mean that the name of a project is up for grabs.
I think there's a good chance (based on my very limited knowledge of IP law), that Gruber has a legal right to "Markdown" as a trademark. However, even if doesn't have a legal claim, he does still have a moral/ethical/community/goodwill/whatever claim to it, and it shouldn't be co-opted by someone else against his desire.
Now, any number of arguments can be made that's he's being unreasonable, stupid, passive-agressive or worse. But that still doesn't mean you should be able to take the project name.
Also, I think there are reasonable arguments that can be made that Atwood acted improperly or worse. Though I do think he's less intransigent (did I spell that word right? did I use that word right?).
I think the current state of things (using the CommonMark name) is a good enough situation, and as I stated before I think that over time, "CommonMark" will become the defacto standard over "Markdown". Both in terms of the software implementation and in terms of the 'brand' this think becomes commonly known as (ie., people will actually say that an editor or whatever supports "CommonMark"). I think this will happen because CommonMark will be at least as good as Markdown (it's probably already there), and there will ultimately be less confusion about the various flavors.