The intelligent way around it is to recognise that John Gruber's rights and license, and chose a path that both respects the limitations he puts in place and allows a community to coalesce around a standardised form of a text format derived from John Gruber's spec.

So the intelligent action is to not call it Markdown, since that requires Gruber's written permission, which is currently a time-sensitive issue, and may be a show stopper later as his format slips more and more out of his control.

Pick a new name, document that it's derived from Markdown (and respects John Gruber's wishes), and create a community around the better specified and test-case based approach to standardisation.

Product prefer using derivative libraries, rather than Gruber's own Markdown implementation. (With or without Gruber's written permission). Pandoc, for example, is a common library for Markdown support, I guess GitHub, Reddit, stack overflow are using their own custom implementations, or implementations that started or during their lifetime became custom implementations.