My suggestion above solves this by at least separating out the military and civilian academies and in the extreme creating an academy type for each officer.
IMO if Steve every implements a change like that you could change it so that academy commandants will make an academy give out only their type.
Also, and this is also buried in the suggestions thread, late game when you have 4k+ officers it takes a very long time to open the commanders menu, this is because the officer filtering/sorting on the bottom right of the screen will automatically filter out the massive list of officers from lowest rank to highest rank.
Either add a "filter" button to make the filtering manual or make it so that by default it sorts from highest rank to highest rank - which keeps the list small much later into the game and improves the speed at which the commander screen opens.