It 's pretty quick to mod in actually; take the player.faction file in ~/data/world/factions and add the appropriate file path for the portrait you want to use. As an example:
"portraits":{
"standard_male":[
"graphics/portraits/portrait_hegemony01.png",
"graphics/portraits/portrait_hegemony02.png",
...
"graphics/portraits/ms_portrait_boo.png",
],
There are probably better ways to do so, but this is the quick, hackish way of doing it. Hopefully it helps.