Seems like its misconceptions. Gangs aren't taking towns, they are intimidating the superiority there into giving them something for Not killing them. Militia by this token Should not be related to them, except to the town. Militia is made up of people from the area, normal people with guns defending their territory. If someone shoots at another wastelander there and not their town, they shouldn't give a shit. In-fact, if a gang shows up to oust the gang which is holding them hostage (because thats what 'controlling' the town amounts to, does it not?), militia I would think would welcome it, because the more dead wastelanders, the better for them. Not to mention that gangs don't actually invest anything Into the controlling of the town at all, except their gear, which they do for pvp anyway and not the towns benefit.
Its not like dead people in the town has their gear go into the stores, which I think would make sense. Dead person in the street, people are going to run over and try to loot it to pay for food and their starving children.
Anyway... Militia should act as guards, and even Fight the gang who tries to take them over, essentially acting as normal guards and then a first wave of defense to the people trying to instigate TC. Militia shouldn't take any orders from the controllling gang either. They are not mercs. As for increasing militia in a town, this should be done by the town itself. Perhaps by its growth (as in how much wealth the traders move there) which lets the mayor/whatever afford to pay for more militiamen to stand guard. This could give rise to more reason for gangs to control towns consecutively, as the longer they do, the more militia will be there to defend their stake during the first wave.