That was my first reaction last night after seeing CJ play so well. But, honestly, CJ needed minutes. He bounced around in different systems in high school. In college he played in probably the worst developmental situation in the country. Last season, he didn't get summer league or even that abbreviated training camp (visa issues).
CJ needed minutes and got 1,000+ minutes in the D-League. Mills, to compare, has played only about half that many minutes with the Spurs. Even if the compe ion was lower, CJ was in major need of repe ions. He's probably better off now than if he was used in that Patty/Nando/Gary timeshare.
Besides, it's really not that late in the season. Seven weeks is PLENTY of time to work in a new player. Especially one who knows the plays and is familiar with his teammates/surroundings.
Looking back, Jacque Vaughn didn't win the job in 2007 until around the All-Star break. This would be a similar move in which Pop forfeits some offensive explosiveness for better defense and a steadier hand.