Basically, after the Writers Strike in 2007-08, Seth MacFarlane took a job at Jon Stewart on "Family Guy" for going back to work during the strike, to which Stewart called up MacFarlane and then started to "rant at him for an hour"
this was during 2007-08 so I am guessing the issue has passed but I dont even remember the jab so have to take a look back at old episodes.
Looks like the source is a TIME interview from 2008:
Originally posted by TIME (time.com)You mock celebrities so often on your show. Do you ever get any kickback from these people? The only two people that's ever happened with me for were Ellen Cleghorne from Saturday Night Live and Jon Stewart. I got a very angry phone call from Jon Stewart.
What did you do to Stewart? There was a very inside joke on Family Guy referring to the fact that he was working before the writers' strike was over. It was admittedly a very direct middle finger of a joke, which I don't discount. But he called and was very angry about it. The call lasted an hour. It was pretty amazing. He's a very good debater, I'll tell you that. It was fascinating to me that it went on for so long.
Someone on Yahoo! Answers figured out that it had to be from episodes 8-12 of Season 6, because those were the only episodes that aired between when the Daily Show came back on the air when he told Time magazine about it. Furthermore, someone else claims it is from the episode "Former Life of Brian" where Brian tells his son "No, no, I'm not going to put myself on the line like that."
If that's the case, I'd say it's a pretty inside reference. I'm trying to find evidence that Jon Stewart ever said that publicly about the strike, and I am unable. Perhaps he said it personally to MacFarlane? Perhaps the guy who said that was the reference is insane?
Man, I just realized I don't watch anything on this network aside from Survivor, Amazing Race and occasionally 60 Minutes. I guess AR's move to Sundays fills that West Wing hole, though this means AR will now consistently be pushed later by football.