Dumb but not thuggish. In fact the view that it is thuggish is feudal, since it implies that the employers are lords handing out favors and punishments to their subjects below, and thus have a duty to be fair and compassionate about it. But the employer is really an equal at the negotiating table. Some people argue that capitalism can be coercive in the relevant way (a point I have no wish to argue for or against here), but it's demonstrably not true in this instance, since Braithwaite was able to walk away from a crummy deal. No doubt the employer was worse off for it. That's how it's supposed to work.
* At hire time provide a list of "my ip" and "ip from previous employer that may be controversial here"
* At personal project start time, get a document signed from management saying "this is not related to $employer, and does not count as related work"
* At exit time (particularly when there is post employment IP or non-compete) get a document agreeing that "this IP was from the employee to the company, this was not.
It sounds like a bureaucratic mess, but it's like 10 minutes of hassle here and there, and saves a bunch of issue, even in the future if say, the company gets bought out and the new owner has different views.
The actions described by the GP are not the culmination of deep legal rumination on the topic.
What a thuggish company, with such a feudal view of its workers! Hopefully most companies understand that they don't own their employees outright.