Ambushes are tricky, they have come up before so search the forum and be persistent, there is some stuff there.
It may be a little laborious but the way to do it may be to use a bunch of doTarget and doFire commands, targeting each member of the target group in turn.
So when the target group reaches the kill zone a script activates which looks a bit like this
#one
mortar doTarget badloon1
mortar doFire badloon1
? getdammage badloon1<0.2 goto "one"
#two
mortar doTarget badloon2
mortar doFire badloon2
? getdammage badloon2<0.2 goto "two"
and so on. That's just a sketch, its not a proper script. You might be able to use forEach to make it neater.
To return to my original answer, it might be easier to place an invisible H in the centre of the kill zone. An invisible H is just an object like a tent. It's just like a helicopter landing H except its invisible ... you're supposed to use it to get choppers to land in the place you want, but it might help you out here. Just get the mortar first to target, and then to fire at, the invisible H. Since its in the middle of the kill zone the enemy will get killed.
Don't place a destroy waypoint on a fake target like the H or something buried. It will as you say only end in farce.
Don't panic - none of this is complicated or difficult, its just a matter of finding the best solution for what you are trying to do.