Like a wise friend of mine said once, this season is all about role-reversals, and he was totally right about that. In season 1 and 2 Sarah kicked ass in every episode, while Chuck had to run and hide. This season Chuck doesn't need his body guards, and of course because of this Sarah's and Casey's roles change too, they are more his mentors now. Sarah's reaction to Chucks change is seem pretty natural too me because from the episode one she has noticed that he has gradually has changed but also seen that he still struggles with maintaining the "old" Chuck.
I've mentioned my problem with the 'role reversal' concept a few posts ago. In theory, your wise friend is not wrong. Naturally, once Super-Chuck was created, there was (potentially) always going to be less need for Sarah and Casey. OK, so technically that didn't need to be a 'reversal', but instead perhaps a role 'equalising', as there should have been no need for Casey or Sarah to then fulfill the 'run and hide', or at the very least, the 'need regular assistance' roles. But of course that had to happen to some degree, simply because drama needs someone to 'rescue'. But I digress.
Going back to the fundamental idea of a 'role reversal' for Sarah and Chuck means identifying their previous roles. So, before Intersect 2.0, Chuck was primarily comedy and Sarah was primarily action. And both shared equal duties on the drama side of things. Since Super-Chuck appeared, Chuck has indeed now adopted the primary action role in the show, supporting the idea of a role-reversal. However, it's no stretch to say that Sarah hasn't
taken over on the comedic duties.
So, it's been less of a 'role reversal', and more a case of 'giving one character more to do, and another character less to do.'