The issue is ultimately the fact that Battler has amnesia at all. Ikuko is necessary as a device to make sense of Tohya being able to function and thrive with serious amnesia. If Battler didn't have amnesia, she wouldn't really be necessary for the story. But instead, a new reason would have to be explained as to why Battler isn't revealing himself. My guess is the author got mad that everyone was guessing Amakusa was Battler nothing the author could cook up made more sense to him than amnesia.
I don't exactly think of her as a deus ex machina, though having said that Ryukishi goes to great lengths to make her seem exotic, magical, ephemeral, and super-powerful, so it's almost unfair to just dismiss her as an unimportant side character.
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