I also feed my CO2 directly into my canister filter (Eheim 2217) and it improves the CO2 levels in my tank (disolves much better).
The gas would have to build up at the top of the filter somewhere, where the impellor is, meaning that the impellor may not be fully covered by water. But I guess at the rate that I am pumping it in it will gradually make it's way to the top of the filter (i.e. a lot of bubbles would get trapped in the filter media itself), so this probably isn't a problem.
The biological filteration seems to be fine too - I would expect that if huge quantitities of the gas were being pumped in it might cause an issue but a few bubbles of CO2 shouldn't cause any harm.
I have been pumping the CO2 into my canister for ages now and haven't had any problems with the filter or the water quality (i.e. no affect on biological filteration).
