Could it not be managed in a Grunt task?

I suppose you could write a grunt or gulp task to parse all of the files after jekyll has generated them and run them through typeset. It might be slightly challenging to ensure that only the actual article content gets ran through typeset and not any other content.

Unfortunately, I use Github pages so this wouldn't work for that from what I can tell.

> It might be slightly challenging to ensure that only the actual article content gets ran through typeset and not any other content.

Not a problem. It accepts CSS selectors as options (e.g., ".article").