If you stat the zombies and militia as minions, they'll drop on one hit from each other, not just from one hit by from the heroes (vs. zombies) or the necromancer (vs. the militia). Whereas if you stat the zombies as minions and the militia as low-level humans/elves/etc., then the militia will rarely hit the zombies, but they'll drop them when they do. That actually might be plausible, but more extreme cases could get silly.
The answer is that when NPCs are fighting NPCs they do exactly what you want them to.
If your players are so anal that they need to know you're rolling, just roll behind your screen and ingore the roll.
Its even easier in this situation because if you have a bunch of zombies and townsfolk you aren't going to want to bother running all of their attacks anyway, you are going to handwave the situation and say "The townsfolk struggle with the zombies, the Baker falls to a lucky blow as the mobs struggle back and forth" then remove a token or two and keep going. The Heroes can then use the townsfolk for flanking, give them bonuses and healing(which you then just describe the effect of during their turn, and move tokens around).
The players are there to be heroes, not watch someone else be a hero. So don't roll for NPC's on NPC violence, handwave it. Just say what happens and get it over with you wouldn't roll if it were off screen would you?[I envision a man sitting in his basement rolling die to see if the goblins capture the barons daughter to determine whether or not the PCs have a plot hook to follow] This is better on so many levels its not funny. Its better for roleplaying because the players have to deal with the situation as you want them too. Its better for wargaming because the players don't have to sit and watch the DM masturbate with all the tokens he has to play with. Its better for everyones time since the encounters go smoother and faster.
In short, there is only a problem because people have forgotten that DnD is about roleplaying heroic fantasy and not a system by which to simulate a heroic fantasy world. No one is going to run a computer model to create and then study the DnD world, rules that figure someone is going to do that are a waste of time, and are another thing that get in the way of the primary purpose of the system. For players to get together with a DM and roleplay.
edit: another easy way to do it would be to set them both as minions and have each side lose a number of guys equal to the ratio of them to us(not including the PCs and non-minions)
So if you fight a force of 25 zombies with 5 townsfolks, the 25 zombies are going to wipe them in the first round they are engaged and 1 zombie will die. If you fight a force with 20 zombies and 20 townsfolk one on each side will die until the PC's or Villains make a difference and one side starts to overcome the other