It's 2015 and I realized that the Wordpress WYSIWYG editor (TinyMCE) is still a nightmare for your markup. C'mon, I don't want to write about code while fighting with ugly pre/code tags. It's 2015 and we have markdown! Unfortunately, the existing solutions are inside a bloated 20MB plugin (JetPack), break with my "old-fashioned" theme (PrettyPres), are too complicated or they are just not maintained any more.
I made a markdown plugin that is damn simple. I'm somehow surprised that nobody else combined parsedown and highlight.js before. And it works like a charm. Fork it on github, it's yours. The plugin is also under review. It should be visible on wordpress.org if gets an approval.
Write this into the editor:
[markdown] #h1 ##h2 text [ /markdown]
and the shortcode content will be parsed with parsedown.
By the way, this post was written in markdown: :-D