Many would say that it is always wrong to kill civilians even if that would result in far less military deaths, since civilians are basically innocent and it is never right to do evil so that good may result. This is even the case if the civilians are nasty people who have nothing but hate in their hearts for the enemy, they are still civilians and as such are not ethical targets of death. That is certainly the position of international law.
For consequentialists the situation could be quite different, since the relevant question is what course of action would cause least suffering overall. A problem with such a strategy is that there is probably a horrible action that would affect the enemy to give in quicker, but just could not be considered ethically (say it was possible to murder a number of babies, for example). Another problem is that it is so difficult to work out what the balance is between civilian and military deaths, and once we start thinking in these terms it is difficult to know where to stop.