I really can't imagine Akai would be so ruthless as to rat out Scotch to deflect suspicions from himself and gain promotion and trust in the BO. I think the circumstances might be similar to what Kir had to do to Akai, except in Scotch's case no one was there to save him. Scotch might have been found out already, and Akai was entangled in some sort of trouble that made the BO suspicious of his loyalty. So maybe Akai was ordered to kill Scotch. (I think this scenario may be unlikely though because Scotch's real name, as Vermouth said, was never found out. This was most likely intentional.)
Another possible scenario is that Amuro was forced to kill Scotch to spare him of the torture he probably would have had to endure so that more intelligence and his real name wouldn't have been leaked. And Akai might have been involved in this as the person who accidentally leaked the info that Scotch is actually a secret police (hey Akai was probably gathering intelligence about each BO member he knows of)