Now, the way I saw it was that every permanent that fell into AM's criteria was hit with a destroy effect, this meant that Player A's enchanted creature, and the enchantment itself, are included, but due to the enchantment giving the creature Indestructibility until the AM resolves only the enchantment gets blown up (as it itself is not indestructible) and the spell finishes completing everything it can accomplish and resolves completely.
It was argued that the creature till has a "destroy" effect on him until the end of turn and that with Darksteel Mutation gone, it is now destroyed.
You were right for the reason you offered. A destruction effect is a one-shot effect, and unlike damage, isn't marked on a creature for any length of time. At the point that the Vengeance went off, the creature had indestructible and so couldn't be destroyed by the effect.
Player A controlled a creature who enchanted with Darksteel Mutation. Player B drops an Akroma's Vengance.
Now, the way I saw it was that every permanent that fell into AM's criteria was hit with a destroy effect, this meant that Player A's enchanted creature, and the enchantment itself, are included, but due to the enchantment giving the creature Indestructibility until the AM resolves only the enchantment gets blown up (as it itself is not indestructible) and the spell finishes completing everything it can accomplish and resolves completely.
It was argued that the creature till has a "destroy" effect on him until the end of turn and that with Darksteel Mutation gone, it is now destroyed.
What's right here?