The article really doesn't call out explicitly: The management engine never stops running, turning it off is nearly impossible, and if you do succeed the computer resets in 30 seconds. So this untrusted entity is constantly looking at everything happening, and the best we can do is load some dummy configuration so it doesn't do anything, or perhaps it doesn't do anything, because we don't know.
Having an architecture without the big brother chip sitting on the bus would be a huge huge bonus.