I could be wrong but I thought that the "dispute" over Conker was that Nintendo of America didn't want to publish CBFD as a Nintendo game because they knew that people would think that a mascot based platformer published by Nintendo was appropriate for children even if it had a Mature rating.
From my limited understanding, at the time Nintendo of Japan determined what games were made and Nintendo of America decided what games would be released and how they would be marketed in the West. Throughout the SNES and N64 days Nintendo of America censored many Japanese games to promote a more family friendly image; and even prevented many games from ever being released in the west.







