As Markdown's "parent", John has a few key responsibilities in shepherding his baby to maturity. Namely, to lead. To set direction.
When someone releases some free software, they have no obligation whatsoever to do anything with or for it again. No legal obligations, and no moral ones. Unless there is some kind of explicit contract the author is free to forget anything ever happened.
It's obviously nice if the author assumes responsibility for further development and leadership and whatever, but it has to happen voluntarily or be compensated.
This is an important difference from the proprietary world Atwood is more familiar with. With proprietary software, the user is pretty much always a customer, and a customer has rights, one of them being that the software works and problems get fixed. With free software, the user is a receiver of a surprise gift.
Now, as far as the Markdown situation is concerned, the facts seem to be that Gruber does not develop the specification or reference implementation, but other people would like things to improve.
In the free software world, the best thing to do in this scenario is to gather the people who want to make improvements, have them collaborate and take over development, thank Gruber, and make the world a better place. Or, vigorously waving a spatula, fork, fork, fork.
There's a whole bunch of people using and relying on Markdown now. Atwood's Stack Overflow site is one of the prominent ones. There's implementations for many programming languages. There's other sites using Markdown. All of these people could (I am reluctant to say should) start a "Markdown Foundation", so to speak, and get to work.