The enemy needs to be destoyed.
Women and children are no exception. Ever, if they are going to grow up and become a threat they have to go down.
Put it this way, your a jedi child, just wathced all the jedi die by anakins hand, who are you gonna go after when you grow up? exactly!
Either that or everybody was a little trigger happy like My Lai in the Vietnam war....orders need to be followed.