Certainly. Cushman's most interesting (but hardly conclusive) evidence is a Roddenberry memo noting the similarity between the two stories. I'm not sure if NBC had received 'Space Seed' by the time 'The Alternative Factor' was being re-written at the last minute. I'd have to check the book (and, if the information isn't there, the Stanley Robertson letters in the UCLA files).
Okay, forget what I wrote above. I misremembered some of it, but just checked the book again.
Roddenberry sent a memo to Coon about his concerns of Masters betraying Kirk in a similar fashion as McGivers betraying Kirk. His objection comes about not so much because of the story element of betrayal, but because the two stories ("Speace Seed" and "The Alternative Factor") were in the works at the same time and he didn't like using the same gimmick twice or at least one so soon after the other. Both story outlines were submitted the same day, August 29th, 1966, so both stories were in-the-works concurrently.
Stan Roberton's objection early on was in regard to an early story element in "The Altenative Factor" that had Kirk meet his mirror universe double. He didn't like it because we had already seen a Kirk double twice in "The Enemy Within" and "What Are Little Girls Made Of?"
NBC didn't balk about the romance until the actress to play Masters was hired and then folks at NBC started making "off the record" phone calls to Desilu. Then it became "drop the romance" or "recast the actress." This was late in the game and so they decided to keep the actress and drop the romance.