I hear org-mode is a good alternative. In the mean time, consider storing a permanent .html version upon publication of markdown
Markdown isn't the be-all and end-all of markup formats, and there are valid reasons for using formats with strict specifications (e.g., AsciiDoc or ReStructuredText for certain kinds of technical writing). But the chances of Markdown documents suddenly being woefully unreadable in 20 years are roughly in line with the chances of plain text Unicode documents being unreadable in 20 years.
Notably, GitHubbers and StackOverflow representatives joined to define CommonMark, but GitHub and StackOverflow do not have remotely similar fenced code block conventions.
Also, CommonMark currently says that they have not yet defined a version 1.0 of the spec.
I certainly applaud the effort, but CommonMark did not unify all the Markdowns.
If your documents are available on the open web, you can visit them on the Wayback Machine to make sure they're cached as HTML. This is in some ways more reliable, and some ways less, than trying to keep track of your own HTML transcodes over decades. It's generally a more reliable way of making sure they're available after you disappear.
The major point of using markdown, or why I use it, is that it doesn't require a working implementation to be understood. I can open a markdown file in ed and still understand it. From what I've seen of RestructuredText and Org-mode, if i'm not using the implementation, it becomes a mess.
(I also always recommend to put anything that isn't widely implemented in Markdown in HTML instead since that will be reasonably parsable for the next couple decades.)