For those not in the know: the "backwardsness" here is literal, not merely a preference. Specifically, the underlying devices are mapped to mountpoints as:
It's wrong, and makes no sense, but it's not the sort of thing you can afford to fix, because so much else depends on it.
Well, you can't fix it as you said due to dependencies, but if it bothers you that much you can always work around it... just create some symlinks to the mount points that make more sense to you. i.e.
ln -s /media/mmc2 /media/internalCard
ln -s /media/mmc1 /media/removableCard