While reading a Robert Sawyer post on Facebook he provided a link to an interesting find: memos from Robert Justman to Gene Roddenberry regarding Harlan Ellison's second draft of TCOTEOF.
It's only five pages, but it's quite interesting and strongly supports the idea that Ellison's original approach was unsuitable for Star Trek.
From what we can see we get a strong sense that GR and company had no choice but to extensively rewrite Ellison' story to make it work. The fact that TCOTEOF is one of TOS' very best episodes---and one of the best examples of SF on television---makes it hard to criticize Ellison's story being so extensively rewritten.
Even more so now I'm intrigued to read Ellison's original treatment just so I could have a better idea of why it couldn't have worked. A story for television isn't a one-man job and a work of holy gospel that cannot be changed. The issue isn't whether Ellison's original was good or not, but whether it was suitable for Star Trek
and what was trying to be done with the show. If something has to be changed for the good of the show then so be it. GR and company obviously saw something worthwhile in Ellison's original story, but they also recognized it had to be reworked to fit into the fictional Trek universe already being established at the time. I haven't read Ellison's book on the subject (I'm going to order it) so I don't know how much of his complaint is him not liking what was changed or him not liking how he was treated (or how he perceives he was treated). Roddenberry has been known to be a jerk at times.
Well, have a look and see what you think.