I think you're suggesting extremely interesting but I'm not totally clear on it. So someone[1] has come up with some code to either disable (kill switch) or remove the Intel ME. (Setting the HAP bit is the kill switch.)
Now Intel and its vendors are going to issue a patch for the Intel ME. Are you saying that as a result of applying this patch we might not be able disable or remove the Intel ME? In other words, we'll end up with a slightly more secure Intel ME, but be worse off since we can't exploit any bugs to get rid of it?
If I'm understanding you correctly, this sounds like the iPhone situation: upgrade to a newer iOS and lose the ability to jailbreak.
[1] https://github.com/corna/me_cleaner/wiki/HAP-AltMeDisable-bi...