I'm Hiding In Your Closet
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I was going to give a much longer answer, but then I realized: It's quite simple. No, BECAUSE the weapon, interacting with the swarm in such a fashion, is only going to interact with a few at a time - a swarm represents countless individual little monsters, and shaving a few off isn't going to represent serious harm to the swarm as a whole. Hence, the reason is basically the same as why immunity to normal weapons is standard for swarms. Unless, perhaps (and here was something I thought about before), alignment-based weapon enchantments specifically work a certain, "non-core" way in the DM's campaign setting, or the monster has a specially-mentioned abnormal weakness (before 3.5, rakshasa were singled out as having a very specific and very severe vulnerability to "blessed crossbow bolts"), a weapon like that isn't going to work in a reactionary or "environmental hazard"-style fashion.