chekov as the traitor could have worked very simply with out many re-writes. think about it. the grand conspiracy's plan was simple, b.o.p. fires on kronos 1, kronos 1 comes back and attacks the enterprise... everyone and their mother would expect kirk to defend the enterprise and presumably destroy kronos 1. enterprise carries on its merry way after and war breaks out.
no one thought kirk would surrender. chang and valeris are flying by the seat of their pants once kirk beams over.
simply have things play out the way they did but have chekov constantly bugging spock to go on a rescue mission (which would also lead to war, and the planned outcome). once kirk and mccoy are sentenced to prison, chekov could come clean and or be found out. and all he really would have done is forged the data banks. he doesnt even need to kill the guys that beamed over to kill gorkon.