So, the moment a believer "exceptions" someone attempting to murder his family, he can no longer claim, in good faith (ahem...), to be a member of that faith?
But killing the non-believer in the name of religion is against only two of the three religions you point out. I do not think that the logical conclusion to the evolution of religious beliefs needs to be "we were once psycho nutjobs," but rather "there were once some psycho teachings in our religion, glad we sorted those out." That way, people could revere their faiths without having to sell them at the end of a sword. And, like you, I can't wait.
Kayla's faith led her to seek out the suffering and bring comfort. It's a sin in the truest sense that she got killed for that.
-V