If I understand correctly, the intention wasn't that when JNT left, the show was done for good. But, rather that there would be a hiatus (a year or so) until new producer could be found. The problem is that there were no other producers chomping at the bit to take over DW. This lead to DW just fading away.But if JNT had left in 1986, effectively so would Baker. Had JNT left, the show would have been over, and he was well aware of that.
I don't believe that Christopher is quite correct when he wrote, "the show left when he did," as JNT remained involved with Doctor Who internally at the BBC beyond 1989 and there were tentative plans for season 27. I think it's more accurate to say that the BBC quietly stopped production on the series while they tried to figure out what to do with the property so as to not have a repeat of the "Cancellation Crisis."
Mr Awe