I think that using morality on PCs in combat and the subsequent fallout is highly dependent on individual groups and players. We can discuss tactics to help the OP without having to resort to "the NPCs' families all hate you now!"
General rules that could help you out:
1. Defense: You want to minimize your losses and keep the units you have at peak operating capacity for as long as possible. I see many disposable units as a slightly better option here than simply making your standard number of units tougher. Each individual loss is a smaller percentage of your entire force, and the PCs only have so many actions. Hell, bait your PC wizards into area-attacking a clump of your fodder just to buy a round or two for your better-trained goons to get their licks in.
2. Offense: The quicker your units can acquire and engage new targets, the better. This pretty much always comes down to ranged weapons being your best choice, because your enemies have a much harder time running away from bullets and lightning bolts. Your guys can fire (or combine fire or set up maneuvers) on a new target without having to move It also speaks well to defense: if half your enemies cannot even engage you, you've cut their effectiveness by the same amount. If ALL your forces can engage the enemy, even better.
3. Reinforcements! This was mentioned upthread, and it may or may not work for you. There's something to be said for a good alpha strike by a shitload of Uzi-wielding thugs, but the more enemies on the field on round 1, the higher the chance your players are going to figure out a clever way you didn't notice before to severely mess them up in one fell swoop. Too many waves of reinforcements and each individual wave won't be any more effective than the previous. They'll just be waves breaking against the rocks.
Sorry if I'm retreading old ground here. It just kind of bothers me to resort to relying on the PCs' reluctance to kill bystanders. Seems to me we can beat those pesky wizards and summer knights with good old fashioned tactics!