Over these first two seasons they've brought up the many different obstacles Chuck and Sarah will have to overcome if they ever want to become a couple. Chnuck's ex, Sarah's ex, Chuck want of a real life aka the life he once had and so on and so forth but they've never really dealth with the fact that though Sarah is by no means Casey she is an agent. They've brought it up of course, Sarah has brought it up before saying that she's an agent and Chuck is a asset. But they've never gotten into the meat and potatoes of what that means.
She shot that Fulcrum agent to protect Chuck, she shot that Fulcrum agent because it needed to be done to protect the intersect, she shot him because it would have be wreckless not to and very bad things would have happened if he had lived, she shot him because she would never let anything hurt Chuck. Chuck knows Sarah has killed before in self defense but there's a difference between knowing and seeing. And actually seeing it then seeing her lie right to his fact about it is going to open up a whole new can of worms. Chuck and Sarah were finally getting back to their post Jill/break-up (even though they weren't ever really dating technically) relationship. Well they were getting close actually, especially during that scene when Chuck gave Sarah that beautiful family bracelet. So touching and sweet! But now Chuck's going to be dealing with the fact that though Sarah is by no means Casey, follwing orders no matter, she is still an agent and their are elements of that which might not always be pretty. Then again if looked at another way what she did she did in part for Chuck.