Bonding has always been around, Winkle.
It was especially valid prior to 9/11 due to the way many airlines conducted training; ie paying not only for the TR, but for the cost of training in its entirety. Back then, when T's and C's were supposedly all the more cosy, there would be an even greater recourse should you default the conditions of the bond, ie you would potentially be required to reimburse a far larger pot of cash.
If you fail your base/line training, or get fired, then the recourse will be stipulated in the contract, but from what I am aware with most companies, you will not be liable for the training costs. Similarly if you get fired, I believe. Clearly this puts pressure on the airlines to select suitable candidates.
The grey area, as you pointed out, would be if the T's and C's change, therefore substantially altering the contract. In such instances, I would assume each case would be on individual merit. The likelihood would be for a new contract to be issued detailing the new conditions, and its up to the pilot to accept or decline. Possible recourse to someone who refuses to sign it would be to get fired, in which case, the bond may become void. I would assume that if you accept new T's and C's, then you've commited youself once again. This is no different to employment law in any other industry. It has been known to get massively complex, and ENOURMOUS law suits have emerged.
Certainly given the choice of being bonded, or having to pay for the TR (and possibly parts of line/base training), I know which I would opt for!