You're thinking about the DR and the alignment taint of the attack as separate entities. It makes more sense if you see them in conjunction. Here is a somewhat logical explanation ...
Angels, demons and devils developed damage resistance to allow them to shrug off common attacks. In response, their foes developed a counter to the damage resistance in the form of a good/evil taint to their attacks that cuts through the damage reduction.
Think of it in terms of body armor and armor piercing bullets. Nobody came up with armor piercing bullets until there was armor to be pierced ... Why doesn't the body armor protect against armor piercing bullets? Because those bullets were specifically designed to penetrate it.