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.
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 :)