Khan's speech to Kirk says that he wants to leave Kirk "as you left me, as you left her
, buried alive... buried alive..."
Whereupon Kirk shows us what incredible lung power he has, as his scream of "Khaaaaaaaaaaaannnnnnnnnnn!!!!!!" is heard all the way through solid rock...
This suggests to me that Marla died after
Ceti Alpha V's ecosystem went to hell.
The full line is this
I've done far worse than kill you, ...I've hurt you. And I wish to go on ...hurting you. I shall leave you as you left me. As you left her. Marooned for all eternity in the center of a dead planet, ...buried alive. Buried alive!
Meaning that Kirk might have saved her, if he had checked back in time after Ceti Alpha Six exploded, in other words before
Ceti Alpha Five became a dead planet? I agree, that makes a lot of sense.
Just to play devil's advocate though, at this point of Khan's sanity circling the drain, in his somewhat unhinged reference to him and her being left there, Khan could simply be raging about having been marooned at all to begin with.