I imagine if Elidisbus really is dedicated to the balance, we will become allied with him once he becomes aware of our actions on the First, that or he'll get killed before that can happen.
I don't expect we'll outright ally with Elidibus, but I most certainly do expect a moment where there is a somewhat neutral face-off, where his previous (nasty) intentions were of necessity, where we realize his role as Emissary is not much different to what Minfilia's role is as Emissary (addressing the balance from their side), just that they're doing the same thing from the opposite side, and how they would interact with each other. That their goal is more about the balance rather than tipping the scales in total favour of their side. No doubt he will not apologize for his actions, merely explain them and put more context on the balance issue.

In short, they'll be the true-neutral (or, at worst, neutral-good and neutral-evil). We're the lawful-good, Ascians are the chaotic-evil, yet all mention of 'good' and 'evil' is simply replaced with 'light' and 'dark', and that neither side is inherently 'good' or 'evil', not when either side winning plunges all life into the exact same fate (total destruction of their world). Assuming we do actively begin to address the balance as WoD's, then there would be next to no reason for Elidibus to seek our death from there. The problem, however, is whether he will still be inhabiting Zenos body when Actual-Zenos and his Resonant powah finds him. If you truly believe Elidibus will die, then that would be the most obvious method.

This whole story is setting up a huge amount of glorious grey areas.

- Gaius, ie. "Shadow Hunter", is actively slaying Ascians. This, ironically, would be a huge scale-tipper towards Hydaelyn for the most part, thus we may need to address it whether we like it or not. That doesn't even mention the past ties we've had with him beforehand.
- Elidibus, whether he is a true emissary, will very likely change his tune with us as WoD's and be presented in a less antagonistic light. Unfortunately, this may not save him from Gaius or Zenos.
- What will be expected of us? Will we have to resort to uncomfortable actions in the name of Darkness? How far have the scales dipped? How far do we need to go to balance them?
- Black Rose. Nothing would sell its dire potency more than having it kill off one (or many) cast members. I fully expect to see these chemical weapons inflict ghastly results.
- How Minfilia's role as a true emissary will effect others. Would there be any form of bias towards her former friends, or will they be shunned. How different will she be?
- Varis and his clear distaste for the fact that Ascians are the spearhead of the empire. While I find it hard to believe we'll ever ally with him, I fully expect him to stick those glorious shoulderpads into the backs of his Ascian peers at some point. Will we then be able to vie for peace ala the previous politics cutscene, or will he truly go full ham for calamitous rejoining?

And so on and so forth.