I sort of wonder if the rejection of John Hoyt was age related; perhaps the suits were thinking younger. Hoyt was 59 when he did "The Cage".
Paul Fix was 64 when the second pilot was shot, so, probably not.
According to Memory Alpha, age was surely an issue.
You are right that it does seem to have been an issue with the show's creative team (and, also, Roddenberry wanted Kelley for the role but deferred to Bob Butler and James Goldstone in casting the doctors in the two pilot episodes), but it doesn't seem to have been an issue with the "suits."
This is why I hate posting via my phone -- there's never enough time to get all the words out!