It can't remove the system libraries, but it can decide not to use them. Yes, this means if you were to open it with any app that isn't protected then you will still be vulnerable, but within the app you're safe.
Uh no, it disable the stagefright library... disabling MMS auto-retrial is something else that I also did, but QKSMS also removed the ability for the app to interface with the Stagefright Libraries