Holy cow!
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Jor-El thought for a moment, then walked over to a shelf and retrieved a small globe. “We can tell him the planet has been destroyed. If he knows where he is from, but believes we no longer exist, then there will be no reason for him to come here except perhaps to honor our memories. By that time, what with the planet’s crude technology, it will still be too inconvenient for him to travel here for such a trivial purpose.”
Is this heresy? *gasp* You're tampering with the central tenet of the Superman mythology! All kidding aside, congratulations on your originality.

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“So then we will lie to him, just like the council lied to the insane when they were all exiled, telling them that they were to found a colony.”
Tee-hee! This explains why the New Kryptonians were so wack! Given the way the NK's acted on the show, the backstory that the founders were insane is so believable.

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“Oh, my son,” she whispered. “My son, my little Kal-El. I am so sorry. Please forgive us. If circumstances were different, we would gladly keep you and raise you!” Her eyes became misty. “Jor-El and I both love you.”
Even though I've accused you of "heresy", you still have the basics of the legend. The reasons may be different but the outcome (at least in terms of Kal-El ending up on Earth) is the same. Of course, exploring those different reasons will make this fic fascinating!

What you are doing with Lara and her POV is extremely interesting. Already she has had a great trauma in her life (having to give up a child, and not just give it up for adoption - she had to send it across galaxies!) I'm assuming that she was never able to have another child, that she miscarried:
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The image of his wife lying in blood, screaming in pain and crying that Rao was punishing her for what they’d done.
You never hear stories about Superman's mother because it's assumed that she perished in the destruction of Krypton. And now, Krypton isn't really destroyed!

And Lara is alive - and now she's on Earth! She'll know that she will have super-powers - how will she choose to use them?

And of course she'll know who Superman is, right away - who else could it be but Kal-El?

And how will Clark react to meeting his biological mother? As he said once before, "It's the not knowing that kills you." What will it be like, to talk with his bio-mother, and find out the true story? (Assuming that Lara wants to tell him.)

Lois? Martha and Jonathan? What will they feel about Clark meeting his biological mother? What will the Lara/Martha interaction be like?

Wow, QotC, what a great premise you have for this story! I'm hooked already. Please post more soon!