Both Safari and Webkit crash on startup
You could try doing an upgrade install of OS X from the recovery partition. It should replace preinstalled frameworks and applications with the initial versions but keep user files and settings in place. I have done it twice so far and it solved multiple issues both times, so I have started to recommend it as a troubleshooting step here, even though no-one ever does it.

Another way to restore the directories for Safari or frameworks might be to copy them from a VM.