I have little doubt that the movie will tell the origin story, though doubtless in a very different way from the first Superman film, probably with more emphasis on Krypton before the fall.
That could be good. I wouldn't mind seeing a whole film about Jor-El and Krypton. Do it as a disaster movie. True, it has kind of a downer ending, but you could end it on a ray of hope as baby Kal-El's capsule is found by the Kents, along with an archive of Kryptonian knowledge preserving the memory of their civilization (and maybe borrow the S:TM/Smallville concept of Jor-El's consciousness surviving as a disembodied mentor program, so there's a sense that the hero survived after all). Then the sequel would be a Superman movie.
Assuming that the audience already knows and cares about the character is a fatal mistake that I'm confident will not be made again with Superman. That is one mistake among many that was made with Superman Returns and also with The Incredible Hulk, I might add, though that was a better movie in other respects.
On the other hand, there are a lot of movies about entirely original characters that aren't origin stories. James Bond didn't get an origin story until Daniel Craig took over the role. Star Trek: TOS didn't get an origin story (outside of novels and comics) until 2009. The Incredibles never gave us an origin for Mr. Incredible or Elasti-girl, though the film could be considered an origin story for the Incredibles as a family/team. Showing a character's beginnings isn't the only way to introduce the character to an audience. Often, showing them in action, already established and doing what defines them, is a good introduction.
One good approach is to introduce an already-established character or organization through the viewpoint of an audience surrogate who learns about it along the way. X-Men did that, not just in the movie (with Wolverine and Rogue) but in most of its animated adaptations (with Kitty Pryde in the '80s pilot, Jubilee in the '90s series premiere, and Nightcrawler in the X-Men: Evolution series premiere). Men in Black did that. Doctor Who did that twice -- each of its incarnations, the one that began in '63 and the one that began in '04, started from the perspective of a human character or characters who stumbled upon the Doctor and the TARDIS and learned about them as they went.
I wonder if that approach could work for Superman. Imagine a movie told from the perspective of Lois Lane. Suddenly this mysterious superpowered hero shows up in Metropolis, she tries to investigate, but this new hick reporter Clark Kent keeps getting the scoop on her. What does he know that she doesn't? That way you get to introduce and explain the character to a new audience, but in a way that isn't just an origin rehash.
This film will probably take a Batman Begins/Casino Royale/Trek '09 approach and re-introduce the character in a way that says: you think you know this character's origin and what he is all about, but really you don't, here is the story as it has never been told before, etc., etc. Standard issue for reviving a franchise in Hollywood these days, but that is because it works.
That's a fair point. Studios are very conservative about their megabudget tentpoles, and would rather go with tried-and-true formulas than experimental alternative approaches.