Nice question, and interesting answers.
This goes back to the good old debate on how to manage warship battles and escort duties in FreeSpace. Personally, due to turret FOVs, storytelling purposes, and event management issues, I prefer to use waypoints regardless of the situation. This way, the FREDder has full control on how the mission is going to turn out, and one major advantage in terms of mission balance is avoiding particular configurations where friendly ships are unable to bring their key armaments to bear on relevant targets (enemy warships and incoming bombers alike).
In poor words, I generally don't order warships to attack each other.