I'm of the camp that says that the Judeo-Christian symbolism is mostly faux symbolism. Window-dressing, basically.
(FWIW I'm writing this as an atheist and a huge fan of Evangelion)
To choose an arbitrary example: Sure, there's a "Spear of Longinus" but there's no real relation to what's in the Bible. In the Bible it's an unremarkable thing, used for a remarkable purpose against a single being, Jesus. Literally any spear (or rock, or whatever) would have accomplished the same thing in the Bible.
In Evangelion... it's no ordinary object. It's a superweapon that serves as a trump card against a variety of beings, none of whom are particularly Christ-like. Oh, and there's more than one. Shinji is somewhat of a reluctant "savior" for the human race, which is vaguely Christ-like, but little else in his story matches up with Jesus' life.
Same with the crosses. In Christianity, crosses mean one thing: they're a reminder of Jesus' sacrifice and the chance for salvation. There is nothing magical about a cross itself; it's just a reminder of events past.
In Evangelion, crosses are over the place. Misato wears a cross, Lilith is nailed to a cross, the Angels make cross-shaped explosions, the Evas are transported on cross-like frames, and people apparently turn into glowy crosses during Instrumentality.
But there's no Christ figure in Evangelion, and nobody seems to be pining for one. They don't even seem to be aware of Christianity for the most part, and are certainly not reverent of it. In fact, it's just the opposite - all the major players in the story seem to be determined to fashion their own fate for man, rather than submitting to a higher power. Ultimately, you could cut and paste out all the crosses and replace them with some other evocative token, and the story would remain unchanged.