That is a wonderful idea.
How about making it so that a heroic crew cannot be converted to the enemy by using the crew insurrection intel attack. Also, there should be a limit to the number of heroic captains in the empire. In any movie or show, there aren't 100 heroic people, there's only 1 to 3 heroic captains, or possibly a single ship with many heroic crew. Heroic ships should get a bonus to maintenance, and be chosen Last to be destroyed if the empire runs out of resources to maintain their ships.
And how about heroic scientists / engineers on board the heroic ship, that have a small chance of inventing some super new weapon or technology in a desperate situation, to save the day?