According to what I've read, "The Omega Glory" was simply a mess from day one (i.e., from the time "The Cage" was selected to be the first pilot). I believe It may be the least distinguished episode of the second season.
I strongly suspect the only reasons this dog actually got produced was that it was written by "the Great Bird" and the production team (lead by John Meredith Lucas by that time) must have desperately needed a shootable script to close out the second season commitment to NBC. Thus, it was produced, no matter how convoluted the story was.
Bob Justman is on record several places saying he disliked the episode.
Considering the story existed all through his tenure and yet was never produced on his watch--even when they were desperate for scripts in the first season--I think we can surmise that Gene Coon (who by the way actually invented the Prime Directive) was no fan of it either. Somehow I doubt if he had stayed on as producer until the series was cancelled if this episode ever would have been produced at all.
And I say this actually liking several things in the episode, such as Morgan Woodward, the use of another Starship, the cool assignment Exeter patch, and a pretty cool fight at the end. But all in all, this episode was a major let down from the high points earlier in season two.