We could use an intervention. Where are the A.D.M.I.N.S. ?
I would prefer Eris herself simply end it. I know that's never a thing but a nice story about a higher order being or beings intervening to just remove that bacteria would be nice. The whole thing could be like a singularity event, where they make 'contact' with Humanity, revealing Sirius is 'watched' by an ancient higher level civilization, something we never saw before. Then Gaia can be forced safe for good. Wouldn't have to be a new faction or anything just a story to justify a reversal instead of a retcon.
How do we know there's nothing more advanced from long ago living inside Gaia this whole time? If it were up to me, we'd add an atmospheric system to Gaia you could enter from the poles, that is a hollow inner surface, like halo but a sphere, not a ring. Put some cool stuff in there, bam...problem solved.