Looks like this is an issue with DoubleWiki (the extension that pulls in an alternate-language page and shows them side by side).

Wikisource is still on MediaWiki 1.17, so we'll want to test this scenario again under 1.18 since some of the LTR/RTL style stuff has changed.

in 1.18 it doesn't solve

http://fa.wikisource.org/wiki/%D9%82%D8%B1%D8%A2%D9%86?match=en

and

http://en.wikisource.org/wiki/Qur%27an?match=fa

Should be fixed in gerrit change 15637 (https://gerrit.wikimedia.org/r/#/c/15637/) by using mw-content-ltr/rtl classes.