Unfortunately, I think this sort of example paints you into a corner. The court is not requiring the company to permenantly damage the product, any more than a locksmith who opens a locked door to assist in the execution of a warrant is damaging the door. Once the court has what it requests it is trivial to reinstall the original firmware.

There is an old saying that hard cases make bad law. This is a hard case. The defendants are both heinous and deceased; they lack standing to resist and few will support such an effort. Apple is a third-party here and is on such shakey legal ground that they are left defending themselves in the court of public opinion because they know they are going to lose in an actual court. Bad things tend to come out of situations like this.