Having Saavik as the traitor would have been a bold choice, and would have made Spock's fury more justified IMHO.
...But what would have been even bolder would have been to introduce this suspicious Valeris character from out of the left field, and then have Chekov
be the traitor!
I doubt Koenig would have accepted that.
It wasn't unthinkable in 1991 that there could be another original series movie after The Undiscovered Country
-- The Ashes of Eden
was Shatner's pitch for the seventh film, after all -- and revealing Chekov as the traitor would have logically written him out of the potential next film. Koenig might have liked the development, but he also liked the work, and I think the potential work would have outweighed the development in his mind.