I do not believe the theory that Miko raped Pekora. I think PekoMiko breaking up was purely a corporate decision. It had too many inconvenient elements like encouraging forbidden knowledge, and causing two flagship holos to fuse under a single brand, overshadowing their other collab combinations. This is what Pekora went apeshit about that year, it fits her profile that she'd be highly reliant on Miko collabs and have a rebellious element due to rising so quickly into popularity. Miko being more professional makes sense as well, as she's a complete veteran and was a holo before Pekora joined. Pekora may or may not resent Miko for not joining her side.
