It was a silly show done by smart people.
An excellent summation.
There is a lot of doubt that Eli is meant to be a Jesus surrogate. Eli only faintly resembles Jesus.
Well, of course. Obviously they're not going to come out and blatantly say this is Jesus; they're going to fictionalize it, make it just suggestive rather than obvious, so as not to offend anyone. (They got a lot of grief from Hindus over their portrayal of Krishna and Ganesh in the final episode of the India quartet, even though that was the only episode of the four that succeeded in portraying Indian culture and religion in a reasonably authentic and respectful way.) But that doesn't mean there was no intention of having him be similar to Jesus. I mean, he was quite blatantly associated with the monotheistic god of later seasons and the rather obvious Judeo-Christian mythology that took over from the Greco-Roman one.
As I mentioned he is first introduced as an avatar - a Hindu concept. He speaks of becoming an empty vessel in order to fill oneself with love - a concept with as many, if not more, Buddhist influences than Christian ones. When does Eli speak of clothing the naked, feeding the poor, or sin? He does none of these things and they were all pivotal parts of Jesus' teachings.
You're being too literal. You might as well say that the show wasn't meant to be set in Greece because the real Greece looks nothing like New Zealand.
Yes, they made Eli a syncretic figure so as not to offend anyone by making him too similar to any real religious figure. But it's rather disingenuous to think he wasn't meant to be somewhat Jesus-like. I mean, good grief, just look at him. His appearance was blatantly modelled on the traditional Renaissance and modern artistic interpretation of Jesus. His name, Eli, is a Hebrew or Aramaic name meaning "my God," as well as the name of a figure from the Bible. He's obviously meant to be a rough Jesus surrogate, though just as obviously they avoided making him too close a surrogate.
It's easy to see the echoes between Eli and Jesus in our culture because everyone is at least fleetingly familiar with Christian mythology, but not necessarily Hindu and Buddhist mythology. But they are heavily mixed into Eli as well. And since they are, it's difficult to make the case that he's supposed to be the show's version of Jesus.
That's just way too all-or-nothing an interpretation. Because he's not exclusively based on Jesus, he's not based on Jesus at all? That makes no sense. That's like saying a cat with black and white and grey stripes is entirely devoid of white. It's self-contradictory.