Not maxing out your players minutes is always a bad idea. Okafor averaged 2.9 fouls per 40 minutes played that season.
It was a reactionary decision not backed by data that almost cost them the game.
Okafor averaged 2.4 fouls per game (not per minute). He ended up with 3 in 12 fewer minutes than his average.
Sheldon Williams averaged 3.2 per game.
Shavlik Randolph averaged 2.9 per game.
Nick Horvath averaged 1.1 per game
All of them fouled out. Their per 40 were all higher, but none of them played close to 40 minutes: Williams - 19; Randolph - 14; Horvath - 8.
As you can see, the refs were definitely anomalous. JC adapted and we won.
There were definitely some games where that absolute rule of his hurt the team. 2002 v. Maryland with Caron, I think. But to point to that particular game with those particular refs... not a great place to suggest it was a mistake.
NOTE: I edited this because I misread Dave's point and missed that he used per 40 stats. Useful in general, but definitely shows how terrible the refs were in this particular game.