The light infantry with the javelin is left unchanged because it's a decent unit that can be useful. It is better than some similar national units (peltast for Arco, for example).
I would love to turn off that one militia type that is currently recruitable, but unfortunately that is impossible. There is an event that gives militia to a nation, so if I modded them to cost 9000 gold, they would have an upkeep of 600 each and getting 60 of those guys via event would mean instant bankruptcy.
The point of the mod is not to turn off all independents, but to leave the better, more useful units in the game. If they crappy ones are unavailable, the AI is more likely to recruit national troops instead of hordes of chaff.
I hope that helps.
