The more interesting question is who ordered those companies not to fly their staff on CX? Beijing, of course. Long-term, Beijing may come to regret their decision to take down CX, as that will hurt HK overall. As a financial centre, HK requires a home carrier with a good network of routes to connect to the rest of the world in order to facilitate business, cultural or academic exchanges. Take that away, and HK becomes very much a backwater. Is that what Beijing wants?
Air China, as a shareholder of CX, could easily takeover CX from Swire in theory, but as a SOE, do they have management expertise to operate a carrier according to market principles and customer service? I am a little doubtful. Air China got to where they are not because of their able management or business acumen, but simply because it was designated a national carrier and showered with preferential treatment from Beijing. They operate to political demands of Beijing far more than even CX. So we may end up with routes to god forsaken places where it makes little sense commerically, but must do so because of Beijing orders, like Ashgabat or Kinshasa. While major routes to traditional hubs like London, New York, Vancouver or Sydney is under-served or cancelled out right beause of political dispute Beijing has with those countries.
Besides, HK would be reduced to a mere regional airport where travelers have to transit to Shanghai, Beijing or Guangzhou to fly to Toronto or Paris. Yes, those major mainland airports are reaching capacity limits, but you must remember they see HK as a rival competitor and would rather see HK fail than let them take up the extra demand they cannot meet.
So all in all, Bejing's move to take down CX would only harm HK overall. Unless that is what Beijing want all along, take a rebellious HK down a peg and reduce them to a mere backwater. Beijing can do so, but that would further damage their international reputation. It will send a signal that Beijing cannot govern a thriving city with basic freedoms and instead drove it to the ground. Taiwan sure will see that as a cautionary tale.