Their assertion is that they do not intend to disable hacked phones, and won't take responsibility for them:
"This has nothing to do with proactively disabling a phone that is unlocked or hacked," Phil Schiller, Apple's senior vice president of worldwide product marketing, said in an interview. "It's unfortunate that some of these programs have caused damage to the iPhone software, but Apple cannot be responsible for ... those consequences."
That sounds to me like a way of saying you'll be voiding your warranty, but I think most people who wanted their phone unlocked assumed they were treading in dangerous ground to begin with. The rule of thumb is to always restore something to factory defaults before sending it in for repair, and with the iPhone the same might be true for updating the firmware as well.
Some are criticizing Apple's statements, dubbing them scare tactics. That most likely is true – but it's hardly unexpected.