Chloe, Jor-el -- either of these deaths could serve a larger purpose or make a lot of sense.
Chloe doesnt have to be chosen as the one to die you know? She could find out about the sacrifice that must be made in order to bring Clark back. If she does, theres nothing stopping here from going to the Fortress herself (cause she knows where it is), and telling Jor-el shell be that person.
Could you imagine the visual of her desperately trekking through the North Pole, arriving near death at the Fortress and calling out Jor-el to make her plea? I think Jor-el would finally learn how valuable human relationships can be in Clarks life.
That death could also teach Clark a great deal, and push Lois in the direction she needs to go.
Jor-el could be divided into two categories (hence the quotes around his name). Lets assume for a moment his life-force or soul are somehow still kicking around in the Fortress, or in Lionel. If Jor-el sacrifices his life force for Clark, you can bet that moment on its own will make Jor-el a loved member of Clarks life. Jor-el could still then exist as the voice of the computer simulation that would train Clark to be Superman. And Im sure Clark would be more receptive to his hero destiny if Jor-el gives up his soul to make him see that point.
Personally I prefer seeing Chloe go. She's got to go eventually (that much I think we can all agree on) and I can't imagine a better way for her to go then choosing to sacrifice herself so that the world can be 'saved' by Clark/Superman. She already alludes to his destiny -- she knows what he's meant to do, she knows who he really is. All that adds up to a heart wrenching moment where she dies in Clarks arms making him promise her he will do great things with his gifts (and in consequence not waste her sacrifice).
That was just a lot of fanfic, but I can only hope thats how they go.