Well, there you go. You're freed now.
Kotori prefers the Akuma to be captured rather than destroyed. Her psionic defense abilities seemed to have a much harder time coping with Amaya when the nepleslian psionic's powers were amplified - her hope is that if she can have the Akuma captured, she'll be able to use the psionic amplifiers herself against stronger opponents like Eve (whom can arguably do worse than Amaya, especially considering Eve's ship has psionic amplifiers too).
If someone can go point-blank and fire a subspace detonating mini-missile at the Akuma's barrier, then people like Asher and Nyton will be able to pour down the heat on the Akuma.
You could also not bother and just pour down as much firepower as you can on the Akuma - it's not invincible and can be destroyed. However, you won't be able to capture it that way, and Amaya will probably die in the process.
If you remember from some way back, Kotori feels she needs to face Amaya herself so to master how to protect others from 'burst telepathy' - eyeblink-fast spurts of psionic power (like she used to slap Asher back into the main corridor). That's why she needs Amaya to discard the Akuma so she can isolate her and fight her by herself. Amaya is, in a way, Kotori's vaccine against much stronger psionic opponents.
Also pay mind to Amaya's order to kill Kotori. All it takes is a spray of an aether machinegun, the slice of an aether sword or a teleport and knife her in the back with an elbow blade to end Kotori's life, at which point Amaya will be able to use her amplified psionic powers against you again. Kotori's exhausted and not too mobile about now, so, the ball is in your court for now.