What's the practical difference of running the CO2 into the filter and running it though a diffuser? If you end up with the same amount of CO2 in the water column it should cause equal harm to the bacteria. I run a external reactor and keep my large high light tank at about 30 ppm of CO2. And I still have bacteria in my filter. People that spread that kind of nonsense are either ignorant or malicious.
Here is an example that will really show the fallacy of this though. Take a room. Put two people in the room. One smoker and one person who is allergic to smoke. There is a fan in the room. The fan points toward the smoker. Seal the room and let the smoker light up. Does it make any difference whether the smoker blows the smoke into the fan or away from the fan?