My tinfoil: she survives, but is mangled/killed soon after so he has a love interest in place when the Talosians take him from the beep beep chair into his own nexus/matrix.

Maybe Pike is haunted by the memory of her, knowing that because his fate is already written he wouldn’t have even been able to sacrifice himself to save her from a horrible death, as parasitic lizards burrowed out from her flesh.