The argument that another source pollutes more as an excuse for inaction is only that, an excuse. It has never made sense and still does not. For one thing, this is not a problem that will be solved by treating just one source of pollution, for another that argument never ever considers whether reducing other sources is technologically, financially, or socially doable. Not to mention politically - it should not be a factor, but it is.
That doesn't mean the BBL is on the right track, it is not in fact. France has already demonstrated that banning short-haul flights is counter-productive. Passengers on short-haul flights are mostly connecting to/from somewhere. If they're told they suddenly cannot fly, passengers who connect to BRU via CDG, AMS, or FRA will not take the train, drive, or ride a horse carriage, they will connect in LHR, ZRH, MAD, IAD, JFK...
What can/should be done is stop adjusting landing charges based on noise (most aircraft are very quiet compared to just 20 years ago) and start assessing a surcharge based on the age of the aircraft. It is a better correlation as to how polluting an aircraft is.
Coordinated EU action over tradable carbon credits is another step. Reward airlines with more fuel-efficient engines and penalize the others. That gets us right back to what is politically doable, because it will raise the costs of fly-away vacations to Spain, Turkey, the Dominican Republic, etc.
The bigger problem with BRU is that it is too close to urban areas, while at the same time badly connected to public transportation networks. Not relocating the airport when they decided to build new terminals instead was yet another opportunity falling victim to the Belgian regions' parochial concerns. Unfortunately, that time has come and gone and we have to live with the consequences.