Well the show manufactures the circumstances the characters react to. The could make either choice the "correct" choice. For instance in the episode The First Duty, Wesley ultimately chooses to tell the truth because it is the right choice. The writers said they had an alternate scenario in mind where the correct choice would be to lie because it protects the team.
Therefore in the show the writers chose to make the correct choice the more morally ambiguous ones in order to show the horrors of war. It doesn't seem to be unreasonable to think that the writers could have made the correct choice the morally "righteous" choice more often. It may not have as much dramatic impact on the viewer, but it would be more faithful to the world the characters live in as established by that world's creator.
TNG couldn't negotiate with the Borg thats true, but they couldn't negotiate with a storm either. That was the point. They were a unique entity without reason.
Star Trek doesn't have to present a war as it would occur in the real world, because star trek is not the real world.