I had a real problem with this episode, but not necessarily the same one others have pointed to. The series established early on that Chuck was hung up on Jill, big time, for years and even as he was introduced to his spy life. While it may not have been seen on camera thus far, I don't find it implausible that while Sarah has distracted and detracted from those feelings, they are still there.
However, some things in this episode struck me as so completely implausible that I found it really hard to get into it. Covert operatives don't carry badges, they can't call random law enforcement agencies to follow the around (In chuck vs. the first date, the SWAT team was CIA), and Chuck has never had any real authority or power over anything. I would love, love, L-O-V-E for there to be an episode where Chuck takes a genuine interest in his CIA role and went through some basic training, but to date it hasn't happened.
Likewise, that Jill could stumble onto a method for an antidote makes sense, but she wouldn't have a clear system worked out, it wouldn't be as simple as it was, and she wouldn't just have the equipment laying around to do it with. Plus I doubt a sterilization chamber could have arrived and been set up in a whopping 40 minutes or so.
I don't mean to hate here - and sorry to those who disagree - but I just couldn't get into it. Chuck is a wonderful flight of fancy, and just as with most sci-fi shows you can only enjoy it if you are very liberal with the logic up front, but the whole poisoning scenario just made me roll my eyes.
Further, I have grown weary of the recent change-up in format surrounding Buy More operations. In the first season we followed Chuck around from his home life, to his zany spy life, to his quirky friendship with Morgan at the Buy More and the merry band of misfits doing hilarious things around them. Now we seem to switch back and forth from Chuck's world and Morgan's world, with no significant show of friendship between them and with Buy More antics having very little to do with Chuck himself. This is unfortunate. Chuck versus Tom Sawyer was a step back in the right direction from prior episodes this season, but now they're back at it with perhaps the least funny Buy More situation of all. As Chuck would say, "Show the bearded guy some love!" (and show the other white shirts less).
Despite all my whining, the episode was still very funny - especially the chuck kiss *not* involving Jill, and I'm interested to see where things go with Jill, though it can't end well. He may get to really explore real feelings for a change, but it's just one more thing he has to hide from his family and friends - can't look like a cheater, after all. Poor Chuck...he just can't win. At least not until the show's had a long, successful run.