I've used DIY CO2 into the inlet of HOB filters, with ok results. The reason I say "OK" is because I think I loose some CO2 into the atmosphere because the filter isn't sealed. You shouldn't have that problem in your setup. (canisters being sealed) I am seriously considering getting a canister filter myself (rena XP2 or XP1, not sure yet) and doing just as you are asking, putting the CO2 output directly into (or near) the filter inlet. I worry a little about noise, as I've seen people complain about noise in canister filters and the culprit almost always seems to be suction leaks letting air into the filter.
If you are fairly handy, and have the stuff to do it, you can make a CO2 reactor out of an old gravel vac tube and some bio balls, cotton balls, etc. You direct the water output from your filter into the reactor top, bubble CO2 into the bottom, and the water and CO2 mix in the reactor and the CO2 rich water flows out of the bottom. I've not done it myself, but I've seen directions and pictures and it seems easy to do. If I have problems with noise I'll do this myself.
I've never had the mixture sucked out of the co2 outlet tube into the filter (and the tank) but I don't know how much more water flow into the filter you would have with a canister filter vs my HOB filters. I have had CO2 fermentation mixture in the tank when my fermentation bottle tipped onto it's side and the pressure pumped the fermenting goop into the tank. It was messy, and made the tank smell like a drunken baker, but the fish didn't seem to mind.