I don't see what the formerly "Standard Markdown" project has done to accomodate Gruber as something done because they accepted that he had a legal claim that they were required to comply with, I see it as something that they did because they thought he made a demand that, whether or not it was mandatory, they felt it was reasonable and appropriate to comply with to the extent reasonably practical without tying things up for the project in an open-ended way.
Its not clear to me that Gruber has any basis for a claim in court here:
1) Its not clear to me that the license applies at all, in that its not clear that writing an spec that abstracts and regularizes the common behavior of several programs (which may or may not be all legally derivative of the one at issue) is a non-fair-use derivative work of the program at issue under copyright law, such that a license for that program would be required,
2) Further, its not clear to me that, aside from the copyright license on markdown.pl, that markdown was ever a trademark and, if it was, that it hasn't been either abandoned or genericized.
Of course, Gruber can sue and try to establish any basis for preventing the use of the name that he'd like.