Hopefully we will find out the circumstances of Joubert leaving the field in the review, but I don't think the 'I don't see people criticising the hooker' argument really holds up in this case, nor does the argument that 'personal' comments are unwarranted.
If Joubert did leave the field to avoid a confrontation with the Scotland players (rather than fleeing a hailstorm of plastic) then it is his integrity and respect for the game that is being questioned, not his competence as a referee. Therefore it is necessary that 'personal' comments may for part of the commentary, if we want to draw a comparison with players actions (and how they were treated in the media) then I think Huget's dive last year would be a good place to start.
As far as tens of thousands of irate fans goes? I'm sorry, but this isn't meant to be an easy job, it's expected for a referee to look both captains in the eye, deal with it.