Kuroko being the voice of reason in front of those three that see nothing wrong with one losing their body was a very nice character moment for her. And I wholeheartedly agree with her!
I'm going to toss a theory that the other Cube wants the original body back simply because it misses it.
Then again we have Kihara Amata who straight up beat the crap out of Accelerator so maybe it's not too farfetched.
The thing about the Kihara is that they never play fair. Therestina used a body suit made with data on Mikoto's powers, Gensei used the Level Upper to give himself several powers, Amata used a device that mimicked Accelerator's powers to an extent precisely to mess with the original's, etc.
So, who knows what this one will pull off?