They could have done an episode where it was literally, either share your stuff or you're dead in the water, and they had to make actual hard choices about Starfleet ethics. They never did because they wanted the crew to stay pure and lovable.
I thought "Scorpion" did that to some extent. Granted, Janeway made the choice to approach the Borg about using their nanoprobes against Species 8472, but Voyager
would have been in a tough spot had they tried to cross the Northwest Passage on their own.
I actually agreed with Chakotay's argument and thought Janeway was out of line for second-guessing the decisions he made while in command of the ship. Whatever she may have thought about his actions, he had the make the decision that he
thought was best, not what he thought she would have wanted him to do.