I'm trying to think, I saw that interview with Piers Morgan and Seth. It was more or so Seth being on the side of the writers when they were on a strike, whereas Stewart decided against it and carried on with his show.
"There was a joke on “Family Guy” back during theWriters Guild strike of 2007-2008 making fun of Jon Stewart for continuing to produce shows instead of honoring the strike. After that happened, Jon Stewart personally called Seth MacFarlane up and bitched to him about it for an hour. "
In the meantime, there's no footage online of the joke that tipped Stewart overboard in order to rant to MacFarlane.