Over thinking, but either way works.
If you put it before the filter, the filter will act as an in-line reactor, trapping the CO2 and absorbing better. Down sides are that it will need cleaning more often as it will be exposed to all the crap being sucked in to the filter, also the filter will "burp" every 10 minutes or so where the gas is building up into 1 large bubble which then passes through the impeller.
If you put it after the filter, it will stay cleaner for much longer. There aren't any down sides to this, it won't give you the same absorption rate, but providing your pipes give the gas enough travel (3ft~) it will be fine.
Forget the thing about there not being enough oxygen for the bacteria, this is probably correct on some level, but insignificant to make a difference.