"...That's a massive loss of freedom simply for standing ground on a fundamental right..." Yes. You are correct. And perhaps the most important thing that could provide you a "solution" is that you/we try to spread the idea of "freedom is a good idea" far and wide.

You see, this is how it could work..... If everyone went to the train station and refused to have their bag checked for example, the control system could not cope with the volume of people defying their orders. (The court system and prison system would very quickly become clogged up).

What would likely happen is this... The severity of the punishment for disobedience would become less severe, until they would only try to extort you $10 for refusing to have your bag searched. No longer would you be threatened with 6 months in prison.
If enough people refused to pay the $10 then they would have to go to court or prison etc. but the court could not deal with so many people so they would reduce the $10 to $5 until most people would pay it.

Eventually, if enough people began to realise that they outnumber the psychopaths and the psychopaths are actually very weak, then people would begin to ignore them.
I think perhaps, that is why it is in your interest to try to persuade as many people as possible to refuse to enable these violent people.................. (I didn't say it would be easy).