If your using the Source code to do it its actually pretty simple, though monotonous. Pretty much you need to go through all of the Module.py files in the SC and press "ctrl + f" and type the factions name and delete anything attached to, this would mean in the troops.py, factions.py, game menus.py, strings/py ect go through all of them and type the name of the faction or sometimes you'll have to type the faction number like "faction_3" for the khanate.
Also dont forget item.py as well you'll need to change the names of any weapons using the same name of the faction as well as any specific faction assignments to the weapon, for instance swadia is the only faction that uses winged great helm in native (aside form mercs i think) but it would still have the swadian faction assignment on it. just like the Khergit sabers ect.
Like i said its monotonous. Make sure you work only on one faction at a time, trust me, from experience, I've made the mistake of working on 2 at a time and wound up with a bunch of errors because i forgot something or whatnot. Hope that helps some. Also there are many other threads covering the same topic fyi.