I followed an enemy fleet and caught up to it when it stopped at its rally point. When I attacked, there was not a fleet versus fleet battle, but it was my fleet versus one enemy ship at a time at the rally point. I had to attack multiple times before destroying the fleet. I don't know if the rally point affected the way combat was handled or not, because a later fight at a different enemy rally point proceeded normally.
I used to have this happen quite often in later stages of my GalCiv II games.