Agreed, and *that* is why I feel Kilrah was morally acceptable while Ella is not. In WC3, your only options are to carry out the Kilrah mission succesfully, or being defeated. If you eject, fail a mission, or anything else, then you're headed straight for the losing endgame where you see Earth being invaded and humanity being wiped out.
In WC4 though, you *do* have another option, which will allow you to defeat Tolwyn without killing the people of Ella. The way I see it, the deliberate mass killing of innocents like on Kilrah or Ella are only morally acceptable if there's no other way to save the lives that yoiu're trying to protect. If there's another viable option (and the option of outrunning Ella is very viable, especially using the Dragon loaded out with leech missiles) , then it's wrong to take the killing option.
Best, Raptor