I have a similar theory: I think that Ella genuinely is dead, but she plans on using the MC's powers to revive her. What we've seen of Ella's inner monologue is that "the one" was being evaluated as a potential host for...something, we don't know. For a while I thought that was the Eye, but we know now the Eye was already with the MC and not something Ella could influence. But Ella did tell Cole that she would give literally everything of herself to her chosen one, in a way that he interpreted as romantic but to me sounded sacrificial.
I think Ella wants the MC to eat her brains. Like he can do with Bailey, and how Bailey now lives on inside his mind if he does. Making him a host for Ella, and giving everything of Ella to the MC. I think that's why Ella baited out an attack from Nyx, not because she could survive it but because it would guarantee an intact corpse for the MC to eat. Ella wouldn't get that with Malik or Nico. She's not waiting for the negative energy to fade so she can stand up, she's waiting for it to fade so the MC can finally indulge his curiosity and eat Ella's brains to learn all her secrets, letting her in in the process.
From there, I'm not sure what will happen. Either Ella is going to just be a presence in the MC's head, guiding him and meaning that combined with Doll Ella on his shoulder he has her in stereo. She did say that she thought the MC would be on her side eventually, maybe she's planning that access to her memories will sway him. Or maybe she'll try to hijack his powers to build a new body for herself, like Bailey said she thinks the MC can do for her. Heck, maybe both, trying the first and then going to the second if she can't convince him.
It's not an ironclad theory, I don't have a ton of evidence for it, but it makes sense to me. Also, it has the fun implication that Cole could never have been "the one", no matter how strong he got, because he just doesn't have the right powers. And things that make Cole's obsession more pathetic are always good in my book.