As of today, the GitHub renders markdown paragraph based on the first character.
A paragraph that start with a RTL character will become a RTL paragraph. Characters and words will be rendered right-to-left the paragraph will also be right-aligned.
This includes headers and lists - the first char after the #, or number, determines the direction of the heading.
If there are consecutive LTR words in such paragraph, they will be rendered correctly left-to-right.
The GitHub inline web-based editor also displays RTL consistently with this convention. So for me currently the GitHub inline editor is a very convenient option.
The default direction can be overridden with HTML as provided in earlier answers.
Some examples can be found here: