Nick,

The filter is most likely a surface coating on the glass (as opposed to a glass with particular optical properties). It "should" be fine if there's no mechanical damage to the surface film.

It's sad that Canon won't touch the lens if it's got water in-between the lens elements. Getting the water out from tiny gaps without leaving (much of) a residue is tricky. However, if their cleaning process isn't going to separate the groups to clean each lens then I can't guess the impact on image quality that will be left. Let me know if you want to try. You'll need a small water pump (preferably impeller-style and new), an aquarium air pump, some distilled water, some methanol, some dionized water, and finally some sort of dessicant (I prefer Dririte). Not all of these supplies are easily purchased at your local drug store. However, as I said, it'll take a week or two but you may be able to dry out the lens well enough to actually get the Canon folks to service it at that point (if it's not actually functional).