It's not just that, but they (Everyone, including the show's Creator) felt that J.D. has been taken as far as he can go as a character, they don't see any more maturity or live lessons being put into him, so they felt it was time for his arc to end.
When the show got picked up for a 9th Season, The show's creator tried hard to fight the studio to get the show renamed (Thus making it a spinoff instead of a new season) as "Scrubs: Med-School". But the Studio didn't want to because Spinoffs USUALLY fail, the only one that didn't was Fraiser.
So, basically, Everyone including the guy who CREATED the show, sees this more as a Spinoff than a new season of the same show, so that's how I'm gonna view it. As far as I'm concerned, "Scrubs" ended with "My Finale".