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So if I understand you corectly, you want to have a smart program (not
necessarily in Javascript) which is aware of the rules of the variant, so
it can parse PGN (properly disambiguating the SAN moves and taking account
of their implied side effects). This then should pepare an intermediate
format of the game, which can be viewed through a dumb viewer written in
Javascript.

Sounds very close to what I already have, and was using in my 'Battle of
the Goths' Championships. ( http://home.hccnet.nl/h.g.muller/goths.html ) I use WinBoard as the smart PGN parser, which then prepares a data file
that is loaded by the Javascript-powered HTML page, and unambiguously
specifies how the latter should juggle around gif images to replay the
game.

Only thing that is missing is buttons to scroll through the game, just one
to replay it completely from the beginning. But I guess that would be a
comparatively simple addition.