Not a huge fan of ST so can't really comment on the episode, (I've seen it though), However, Ellison probably wanted to use the concept of 'marooning" which was a thing practiced occasionally by naval and pirate forces for several hundred years.
Ben Gunn is the most famous in literature.
From just having a google it seems Ellison wanted the episode to reflect a proper military ship with some of its crew up to no good, which Roddenberry obviously rejected.
Scotty dealing drugs...
Ellison could start a fight in an empty room and would have certainly considered his work as art as he hated the term Science Fiction Writer. Also at the time TV shows such as The Twilight Zone and The Outer Limits could be considered art.
Ellison had a considerable body of well-received work and won numerous awards. However, it was his way or the highway and that just would not have worked with a show of recurring characters. Also as you say the impact on the budget was enormous and Ellison was just plain awful to be around sometimes.