He remains holding onto the toast he had started to bite into.
imprimatur13: Shinji's overwhelmed, because he's been given the cold shoulder by the one person he was beginning to feel loved him. He probably worries that his sarcastic remarks from before are the cause of this distance.
thewayneiac: It looks more to me like he's just shocked at her business-like demeanor; sort of the same look Dilbert would get if he caught Wally actually working.
ath: Look! Someone accidentally mentioned Dilbert on Evageeks, finally giving me a valid reason to post a link to the legendary New Products Evangelist in the Commentary!