Sabreblade's suggestion is pretty good. However, it has two possible problems. Firstly, you'll have bodies disappearing from right in front of you, which will look odd, and secondly you sometimes get problems with doing things to units that are dead.
Might be better to leave the dead where they are and use createUnit commands.
Alternatively, just place everybody in the Mission Editor but make the enemy "HQ" quite far away. Distant units cause much less lag than close ones. I wrote a wee tutorial on reducing lag once, it must be in the Ed Depot somewhere. You might get some ideas from it.
You'll make the mission more interesting and more difficult if you do things like make the axis of attack different for each attacking group. That way you will need fewer attack groups.
Remember to give the player a time and place to rearm and heal.