Oh yea umm, ofc no one would do such heresy but Yea killing the evil necromancer (which is as we know as Cocona) then you will miss a Great chunk of her story line.
most of the time when the killing evil necromancer conditions even happen you are not even trying to kill her in the first place but she gets killed by the orkind instead so that is a way to unlock the achivement then reload save and try more to rescue the precious cupcake