You want a rational argument can be made against “Thou shalt not kill”... i'll give you one.
First off, if you are reffering the “Thou shalt not kill” as one of the Ten Commandments of biblical fame, that is not one of the original ones. It was added by an Anglican offshoot. So by claiming favoratism for “Thou shalt not kill” as opposed to the original “Thou shalt not murder” you are endorsing/promoting/establishing one sect or group of sects over others. This is a Constitutional problem.