But is the captain shielded from liability if they make the wrong judgement call when deviating from the rule book in an emergency, and protected when following the rules? Or are they judged for making the wrong decision regardless if they were following the rules or not? Or third option, if in an emergency they are protected no matter what decision they make, as long as the decision could be considered reasonable based on information available, even if not optimal based on hindsight?

Of those I like 2 and 3 the best. For 2, it can help influence them to make better decisions (i.e., seek more training ahead of time). For 3, it seems to be the most fair to the person in charge.