I'm putting my money down – right now – on the idea that Cortana's mental instability plays a key role in defeating the Prometheans. My bet is that her "illness" will be directly responsible for:
A.) Destroying or disabling the Prometheans
And in the process:
B.) Save her rational self from her continued descent into insanity
C.) Give her a real body to inhabit (those Prometheans have some pretty advanced AI constructs - if anyone can master a metal/biological fusion, it's them.)
D.) Finally give the Master Chief someone to love.
Honestly, I doubt this storyline will be her last simply because she's become the primary teller of Master Chief's tale.