I had a feeling NBC wasn't completly sold on the show's demise. Why fire the showrunner on a show you know is getting only one final season? But to be honest, they might also have been worried about legal trouble from Chase if Harmon had returned.
It was brought back as a mid-season replacement, essentially. If other shows on NBC had done better, Community would've been burned off in the summer. They had contracts with the actors, who would've had to been paid regardless, so why not have these episodes ready to go? And if the new show runners could turn the ratings around....
Basically if Animal Practice had been a hit--lol--Community wouldn't be on right now.