Are they getting laid off though? Or are they just upset about change even if management has accommodated them? Having lived in Belgium for a long while earlier this century, it's almost certainly the latter.

In fact it's actually explicitly stated in the article (translated to English):

Management and trade unions reached a preliminary agreement on Monday in the negotiations regarding transition measures, working conditions, and support measures. An internal trade union document reveals that the plan provides, among other things, for average salary increases of 16 percent for air traffic controllers, a fixed monthly salary increase of 254 euros for technical and meteorological staff, and a salary cap bonus for statutory personnel. Furthermore, there would be, for instance, an additional mileage allowance for three years, on top of the existing one, and those moving closer to the new center in Namur could receive two days of leave for the move.

For reference, Namur is almost equidistant between Liege and Charleroi at about 45 minutes by car on the interstate (autoroute E42)  or by train (2 express IC trains per hour and more during rush hours). 

This doesn't exactly reek of management screwing over the workers, and it certainly doesn't justify disrupting passengers who have nothing to do with it (hope none of those impacted were traveling last minute to see a dying loved one).