I started to work on this a while ago, but didn't have time to finish it. As this is a needed and useful feature, I'm asking here to seek attention from other developers.
Cite should support directionality for references. It can be accomplished by adding a new param to the <ref> tag like this:
<ref dir="rtl"> ...
which would make the output LI elemnt to render like this:
<li dir="rtl"> ...
In order to make sure the margins and paddings of the LI elements are rendered correctly, I suggest using a CSS class for it like <li class="rtl-reference"> .rtl-reference{ direction:rtl}
Also, "ltr" should be supported too (to be used on rtl wikis). The default direction will be that of the wiki, of course.
Link to discussion on Meta about implementation approach: https://meta.wikimedia.org/wiki/Request_for_comment/Displaying_LTR_citations_on_RTL_wikis