If they were standing by to do so, then yes, they would be able to take action in a timely fashion. (It is a standard practice on some ships to have such personnel standing by during high-risk situations.)
The question is how much time does it take to realize what the emergency actually is? I'm sure the protocol for "X is broke and doing Y" is probably much different than "X is not broke but is actually being controlled by someone else who may also have control with other systems"
Yeah if they control the systems you use to navigate and assess the status of the ship you might not notice it isn't under your control for quite a while.
