Under the circumstances I think it's a minor miracle the warp core apparently didn't breach.
Then again, maybe Khan ejected it beforehand because he wasn't feeling completely suicidal.
Warp cores don't breach in this universe unless you really
want them to. Even with the torpedoes: Scotty wasn't worried about them causing a warp core breach so much as the torpedoes affecting the containment field and allowing the reactor to irradiate the entire crew.