Jeff Atwood and co have done nothing but praise Markdown. They've worked really hard to flesh out a starting point for a standardized Markdown implementation. I think the word they chose, "Standard" makes perfect sense here.
Instead, both John Gruber and Marco Arment are acting super immature about the whole situation. Reading their Tweets today I keep imagining them stomping their feet on the ground because someone did something they didn't approve of.
I don't mean to add fuel to any fire, but I really think we shouldn't be validating their overly-dramatic behavior. I'm sure that Gruber could have politely sent Atwood an email or even public tweet asking that his project reconsider a better name, maybe even calling it something like "Rockdown." From everything I've read so far, Atwood seemed to want Gruber on board but got crickets instead.