The simplest method of "fixing" militia that I can think of is making them count toward population when calculating how much food is consumed in the region per turn (with the possibility of going over the regions max pop.). Then it becomes a matter of balance, as even a region that normally produces a surplus will eventually run into a deficit if enough militia is piled in.
Personally, I never saw a problem with militia. Skilled infiltrator attacks, starvation tactics, and simple smashing with mobile troops make them more a speed bump than a threat.
You obviously haven't dealt with the amount of militia we're talking about. The fact that you even mention smashing with mobile troops shows how ignorant you are on the subject. Most realms simply don't have the nobles to support an army of that size. A decent army for a small to mid size realm these days is 15k CS, 20k if you're lucky enough to have extremely good regions. Even Sirion at the start of its war with Oligarch was only supporting a mobile of around 35k I think, and when 20k CS of militia is put into rural regions, let alone the townslands and cities where there are fortifications, trying to brute force your way through them just leads to the enemy mobile cleaning up what's left of your army.
