You're both right. They wrote and shot that episode before a 4th season was confirmed, (remember when they were on that hiatus?) So they wrote it in a way that would be a somewhat satisfactory ending incase the show had to end there, but still left things open for a 4th season if that happened. Like when Futurama "ended" with "The Devil's Hands are Idle Play Things", and then "ended" again with "Into the Green Yonder".
I think for a lot of die hard fans, season 3 of Community is going to be viewed as the "true" ending, in the same way that Scrubs ended with season 8, and we pretend that season 9 (later subtitled because fan reaction was so insistent) doesn't exist.