No, the raven can't save - according to the spell description, anything that close to the runes when they go off doesn't get a save. Since it has Improved Evasion and was not helpless, it only took half damage. It if it had made its saving throw, it wouldn't have taken any damage at all.
The strip has been breath-takingly dramatic for several issues now, so this conclusion to the current drama is like a joke on the reader, as someone has pointed out. IF Xykon is destroyed, he will simply be reformed in some unknown parts. Since he doesn't breathe, under the sea is as good as place as any.
I guess now there is an inevitable showdown between Xykon and the MitD over the fate of O-Chul, or something like that. As I've said before, I think that V should have broken free from the Mass Charm Person spell before Xykon returns... He still has some lower-level spells left.