Yeah,
I've been expecting her to die since she found out about Clark's secret. For one thing, it's getting weird having Clark be with Lana but confiding his trust in Chloe. Love = Trust, etc. Second, there is the over-arching theme of Superman that he has to bear this burden alone and having Chloe alive is screwing that all up. Finally, as you stated she isn't really in the Superman lore anyway, and to bring Lois into that group is one too many women competing for Clark's affection in my opinion. I think it would make writing difficult.
The more we talk about it, the more convinced I am that it's going to be Chloe rather than Jonathan. What I am trying to figure out is how that life will be taken. Was Jor-El speaking broadly/metaphorically in saying one life being given for another's, or is it a direct cause-effect?
In other words, will there come a time when Jor-El acts to take another's life, the way he acted directly with/through Jonathan to bring Clark back from Metropolis? Or is this an ambiguous "it's the way of nature, so prepare for the inevitable" where somebody like Chloe is going to die because she knows Clark's secret and gets placed in the inevitable position of having to choose between dying and revealing Clark? In that case, Jor-El would be more in the position of "I told you so" than he would be actually causing someone to die. Is Jor-El predicting the future or declaring his intentions?