Wait she said they had decided on disposal and then said espers will be integrated into so...

I think by disposal they mean post war similar to how you treat guns after the war. Dispose not to kill but since they're no longer "necessary" then they have to be repurposed or discarded, in this case they chose to integrate them into society.

Ig they are disposing of them by wiping their memories and letting them live in a society for saving humanity.
And who would kill their super human army knowing that those Gates might appear again?