Not yet, as far as I'm aware. Changing the faction colours is a 'high priority' request at present.

BTW - anyone know the exact RBG numbers for each of the 20 factions ? If so, please let me know (if we know this we can scan the files, possibly medieval.exe, so see if we can spot a table of these colours and see what happens if we mod it with a hex editor). Worth a try ?