A bubble of CO2 here and there doesn't starve aerobic bacteria of oxygen. CO2 and O2 are not mutually exclusive. Adding CO2 doesn't reduce the O2 content of the water. It does lower the pH, and there are discussions about how that affects bacteria, and some think it's good for them and others say it's bad. I think the difference between adding the CO2 before or after the filter is negligible, considering the water flow that's going through the filter.
One word of wisdom though... the amount of CO2 that you get into the tank by bubbling it into the AC Mini inlet is minute. You observed right that the bubbles are chopped up by the impeller, but if you look closely you will see that most of them just bubble to the surface at the inlet side of the filter.
One thing you can do is to decrease the flow by moving the inlet towards the - sign. CO2 will then collect in the elbow of the overflow, and is more efficiently dissolved by the passing water. However, if you move it too much to the reduced position, and your CO2 production is too high, it might airlock after a while.