Markdown is written in Perl. Standard Markdown has released implementations in C and Javascript. It seems unlikely that they are using Markdown code, therefore I don't think they are bound by anything in the Markdown license.
Now we get into the question of whether an abstract API can be copyrighted -- we all assumed no, although the Oracle v. Google case (about Java), suggested an abstract API could be copyrighted. With, most of HN thinks, fairly disastrous consequences if that holds as law, although I think it's probably going to be litigated more.
I frankly doubt Gruber was assuming that his abstract (poorly specified!) API for Markdown could be copyrighted. And almost everyone on HN seemed to think it would be disastrous if that were the case regarding Java; it would be somewhat hypocritical if the same people think it somehow ought to be the case regarding Markdown.
It's too bad because I actually really like this, but I think it's not going to take off because of all the courtroom drama.