Harlan was not happy with the final produict (big shock)
Gene Roddenberry rewrote it considerably from Ellison's original script, and unsurprisingly
Ellison wasn't happy with what the Great Bird of the Galaxy had done to his baby.
Truth be told, while it was a good piece overall, it had elements that did not fit into
the established Star Trek world and a few things (like drug dealers) who the censors
at NBC may have removed anyway.
The details here:
http://en.wikipedia.org/wiki/The_City_on_the_Edge_of_Forever