They felt that Masters betraying her commanding officer and her oath and responsibilities would seem too much like Marl McGivers' betrayal in "Space Seed," particularly since the previous episode happened not long earlier and in the same season. I didn't get the sense they outright forbade the romance and the betrayal element, but they didn't care for either.
'Space Seed' was actually the 23rd episode produced; 'The Alternative Factor' was produced 20th.
I'll have to re-read the chapter in question and respond in more detail.
Much (but it doesn't look like all) of the chapter is here: