The correct fix for this is to convert he.wiki to not use templates to generate ref tags, but that is blocked on support for allowing localised tag names (T30980).

I'm not sure it's worth trying to come up with another hack in the meantime.

It took exactly ten years to add css class to ref tag for rtl support. :-)

From the parser side, i think I'd prefer supporting template-generated tags properly, rather than making tag parsing locale-specific. Using templates for localization works both for localizing "global templates" as well as localizing tags, so it seems worth making our template system work better rather than invent new parser features. More at https://phabricator.wikimedia.org/T30980#3618579

You do aware that reference templates are not used for localization only? Even enwiki has them, as far as I remember.

It worth to fix the issue independently of T30980
Sometimes templates adds references for other reasons - see example in enwiki: https://en.wikipedia.org/wiki/Bcl-2