First, if we consider what purpose the Militia serve, and consider which purpose they should serve, we can determine if they're serving that purpose and we can set a clear goal: making Militia function as intended, or as conducive to their purpose as possible.
Quickly, the question becomes, "How do we make the Militia the way we want them to be?" and to answer that we must define "the way we want them to be."
Analyzing, the first step is understanding the community's needs. In this case, the militia is clearly not powerful enough to fend off competent players, regardless of their numbers. I have personally went to all towns owned by TTTLA and Netwars and routinely killed their Militia solo, so the militia is not protecting the towns from competent players. This means that the militia does not prevent the town from being taken over by another faction, which is implicitly a requirement of them, as otherwise they would impede a main game mechanic; town control. What the Militia currently do, however, is establish a competency requirement for taking towns. This encourages a competitive environment, where Town Control will be between adequately competent factions.
Expanding, if Militia serve the purpose of preventing incompetent players from taking towns then they should serve that purpose as well as possible without impeding other mechanics. For this, the Militia should not respawn during Town Control, and they should not be able to be obtained at all during Town Control, the contending faction having already passed the competency test. Next, we must consider player competency and define it, so as to control the strength of the Militia and, therefore, the competency of Town Control participants. This now becomes an issue of balance which can be weighed upon clearly by answering the question, "How strong should the militia be?" and superrationally considering the answers. Assuming this is done, now the Militia must be accessible for its purposes, which is after Town Control where the towns are no longer contended.
I recommend the following:
No respawn or acquisition of Militia during Town Control. This ensures that Town Control will be between players, not NPCs.
Immediately after Town Control, Militia start spawning at progressively increased intervals until resting at a constant. This ensures that towns can be contested immediately after a town is taken and factions not discouraged from being contesting towns immediately after they have been taken, encouraging PvP. Eventually, this ensures that incompetent factions cannot contend. An equivalent system serving the same purpose better would be ideal.
I think the Militia are fine as-is for their power, not accounting for respawns or otherwise acquisition. I say this considering a possible bias as someone with no issue soloing them, as I've seen worse players identify Militia as insurmountable, ensuring at least some semblance of their purpose being fulfilled.