Read the decision. It specifically makes it lawful to circumvent controls designed to block jailbreaking. It would be unlawful for Apple to deactivate your iPhone for Jailbreaking.
This is a complete misunderstanding of the ruling and the law. Neither applies to Apple or any other company or constrains its actions at all. All this exception does is prevent your being criminally prosecuted for jailbreaking. Period. It does not guarantee that you will be able to jailbreak or prevent Apple from trying to make it difficult or impossible to do so.
Also, Apple cannot add verbiage to the contract to circumvent this ruling. Nor can they add provisions that allow them to deactivate your phone.
1) Apple would not be circumventing the ruling, since the ruling only prevents criminal prosecution for jailbreaking. You are right that they could not make it a criminal offense to jailbreak by changing the contract or license agreement...but I'm pretty sure I didn't suggest that it could.
2) Apple would not need to change your contract, only their license agreement. Apple can make and changes to its software and its license agreement that it damned well pleases, including terms that make it a violation of the license agreement to do perfectly legal things with it. You don't have to accept the new conditions or the changes -- you're free to keep using the old version under the old license.