They'd have to effectively close down the Czech branch of the company.

There used to be shenanigans where an owner would shut down one company and continue as another but goverment labor watchdogs have gotten wise to such methods. And it would be ridiculously overt for a corporation like Microsoft especially under these circumstances when they're in the full spotlight.

No, they'll try to "lobby" the politicians as usual and push for union-unfriendly legislation, try to limit union applicability to certain industry branches, and if all else fails pull out of Czech Republic and hope the rest of Eastern Europe doesn't follow suit.