He did the right thing by keeping Jefferson in. Jarrett Lee is a sitting duck against Bama's defense. He can't avoid the pass rush, or run the option game. The option game was LSU's only chance to run the football against Bama.... and even that is hopeless.
Jarrett Lee would've thrown multiple picks. He only completed 3 passes last time and 2 of them were interceptions.
There just aren't any good options against a defense as dominant as this Bama defense. You'll live a long time and never see a defense this good in college football again.