Stackedit has built-in config option of RTL direction, but that’s not very convenient unless all your docs are RTL.
I’ve been using <div dir=rtl markdown=1> … </div> around Hebrew docs.
many tools support that on convertion to html (IIRC I used retext and pandoc).
retext is convenient for editing mixed-direction source (as long as you put opposite direction parts on separate line).
In any case conversion to non-HTML is harder. In current landscape I’d try writing pandoc filters that understand <div dir=rtl>.
BTW, github does (currently) support dir=rtl in markdown rendering — but does not support markdown=1:
https://github.com/cben/sandbox/
However, it works fine in github pages processed by jekyll: https://cben.github.io/sandbox/README.html