In the good old days, whenever that was, airlines required new joins to be bonded for a sum of money. No money was paid up front but if the pilot left before the end of the bond period then they were liable for the outstanding amount.
Then someone left a company within the bond period and refused to pay the outstanding balance. The company concerned found that bonds were virtually unenforceable.
Companies then went to a pay upfront but get refunded at the end ofthe bond period to pay upfront and pay for the rating training etc no refund.
In general the process is to ensure that the company gets its monies worth and covers all the costs associated with hiring and training a new start.
Having signed a contract both parties are obliged to honour it. The company to pay for your labour and the pilot to supply that labour. Usually a breach of contract by either party allows the other to persue for damages, lost labour outstanding training bonds etc.
If you sign a contract as a pilot the usual notice period is 3 months, if you leave without giving that notice period you are in breach of contract. Simple as that.
So the company concerned is obviously alarmed at the large number of pilots leaving it's "utopian" company and has produced a knee jerk reaction.
Whether that knee jerk reaction is legal, ethically or morally acceptable or not, is a different matter as an employee you are in the first instance obliged to honour your part of the bargain.
If you feel that the contract you entered into is illegal then a, why the ******did you sign it? b, do something about it and get the lawyers involved.
Finally if your behaviour in the last weeks of a contract is causing disruption to the company then do not be surprised that the company takes action against you.