The permanent solution to the flaw is either a hardware/OS-side fix (i.e. disabling this particular kind of speculation via a chicken bit, if there is one), or Safari implementing site isolation in the same way Chrome and Firefox are already doing.

But as the former might well be impossible (at least without ruining performance or requiring a hardware swap), and the latter might take a while, websites should still take the precautions they can. It's a good idea for other reasons anyway: Why keep around an inter-context messaging mechanism you possibly don't even need?