Ahahahaha! Sakes alive, I'm glad I saw DeFoe in that movie before I saw him as the Green Goblin, or for that matter Harvey Keitel as Mr. White. "Jesus, when you're speaking in the temple, and some Pharisee steps up to you who thinks he's David, take your walking stick and bash his nose in".
The meaning behind TLTOC, and how it relates to "Donnie Darko", is that Christ has a vision of coming down off the cross and living out a full life as a normal man. In Darko terms you could say that he lives a parallel life in a parallel universe. Only by seeing a clear vision of his future path does he realize his proper place is to die on the cross. In the same way, Donnie has to realize that his place is in his bed the night the airplane engine lands on his house. He is spared so that he can choose to sacrifice himself, in the process realizing that the love in his life is real and means that in a spiritual or emotional sense he will not die alone. Hence the smile on his face.
Of course, Kelly could just as easily have related his hero's crucible to "Superman II", but it's just a whole lot cooler to bring the big JC into the mix.