The answer to any of the "WWYD if the Capt wants to break preflight rules" questions is:
1) Politely remind the Capt of the requirement.
2) Politely insist that you won't proceed with the flight unless the requirement is met (checklist followed, CVR circuit breaker in, bottle to throttle rule followed).
3) Depart the aircraft and call pro standards if necessary, after informing the dispatcher that the flight is delayed.
In flight issues require a little more finesse, because you aren't going to strap on the chute just because the Capt won't run the checklist.
1) Politely remind the Capt of the requirement.
2) Ensure the requirement is met to the best of your ability without endangering the flight (i.e. run both sides of the checklist time permitting).
3) Ensure the remainder of the flight is conducted as safely as possible.
3) Upon arrival, call pro standards if necessary.
These type questions are really a way for the interviewer to ascertain if you have the strength of character to respectfully challenge a bad command decision, and to ensure that you will take appropriate action to follow company policy and act as a barrier to an accident. Your answer should make plain that you will respect the Capt's position, while ensuring passenger and crew safety. You need to communicate that you won't begin a flight until the matter is properly resolved, and if the flight is in progress, that you will take appropriate action to ensure that it ends safely. Stress your adherence to company policy, and your use of good CRM procedures to resolve conflict.