There is definitely a subtte trolling factor on our name, no reason to hide it. But it does not affect to the fact that moot.it is a damn good name for a product like ours. In case we get popular (which might be the case considering the title of this Hacker News post) this trolling factor will decease.
Speaking strictly about the branding I really think it doesn't matter whether the inherent meaning is closed or open. Product naming is an art form and it doesn't have to be realistic.
I hope we can use Moot successfully on our issue tracker
So we can "close the debate" on those moots :)
If Moot were trademarked by 4chan (now there's a laughable proposition), there really would be a case - and a pretty strong one, at that. As it is, I imagine you're right that Moot has no real case against Moot.it, but it also sounds like the letter made no specific C&D demands.
I imagine your product can rise above this based on its merit, but you gotta acknowledge the subtle trolling inherent in the name. I understand why you can't publicly acknowledge this, but it's there anyway.