What are the chances of the cracker finding the exact combination of ports to knock on, and then the exact key to use? If they're able to do that then they are a dedicated attacker and they're mitm'ing a presumably encrypted connection on your network, so you probably have more problems than just one bad machine, they already replicated or replaced a certificate on your machine, or worse.
And if you then expose a service that isn't via the port knocking algorithm, surely that would show up?
> We're not even comfortable with long-lived keys anymore
Can you not just change the key N number of logins and factor in 2FA as well?
I'm not sure how port knocking cannot, at least theoretically, be used in conjunction with the other measures you talked about.