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.