I just logged on for the first time in a few weeks to ask this very question (I am a big newbie). Funny how the world works.
In my first few games, I won by points after disengaging my whole fleet, but since we were just setting up our ships and shooting at each other it made sense to us. (e.g. fleet warps in, kills as much as possible, warps out).
In our last game though we played a Planetary Assault where I lost badly in the actual battle, but I managed to disengage before my opponent's capital ships/transports could reach the planet. So in the end, I scored ~400 VPs (rounded up gives -1 Assault pt) and my opponent only had ~750 VPs (rounded down gives +1 Assault pt, +1 for the one he scored during the game). So despite abandoning the planet, I technically achieved a complete victory (0-1 Assault pts) which didn't seem to make any sense, considering most of his troop ships were still alive.
I conceded of course, and we discussed the possibility of house-ruling the scenario such that if the defending fleet disengages, the opponent "scores" (counts as having landed troops) once for each transport (+2) and non-crippled capital ship (+1) on the board.