When I really take a moment to think about it, I could see them giving you the option of choosing which Legion your reneade is from, since it doesn't take up much space. Though I think the Career itself might see its advancement chart trimmed down a little to accomidate for it, evening out in the end.
Though I can't see the Thousand Sons being one of the core ones, considering that they're all either sorcerers or living suits of armour. And that just strikes me as requiring too much rules-wise to include in the core book (though I suppose sorcerers would be easy, so they might be in), but if they weren't in the core, I'd definetly count on them being in a supplement.
Reading The Hunt for Voldorious, I can definetly see the Alpha Legion being in the book, as they favour the kind of subversive strategy that fits in well with demagogues and sorcerers, when trying to subvert a loyal imperial world. In fact, I'd go so far as to say that I'd be surprised if you couldn't choose them (assuming Legion is an issue).
But as much as I believe my theories to be likely at times, I've been wrong before. Case in point, rules for playing Grey Knights in Daemon Hunters.