"You could parachute [Sam] into an island full of cannibals and come back in 5 years and he'd be the king"
 “But I have guns, gold, potassium iodide, antibiotics, batteries, water, gas masks from the Israeli Defense Force, and a big patch of land in Big Sur I can fly to.”
 "Graham said, “I asked Sam in our kitchen, ‘Do you want to take over YC?,’ and he smiled, like, it worked."
So in the context of Yishan's comment, it demonstrates to me that the "joking" was a subtle nod that he wouldn't have any qualms with back room dealing and manipulation to reach a goal.
While that might sound like a hit on him, it's actually not. I relate to that approach strongly, and think it's actually the right way to play it.
However I think it's actually a bad comparison to say he's the "nicest guy in the valley." That title goes to Steve Wozniak.
 These are for survival in the case of an apocalypse, not aggression
 Graham loved Sam Altman, so he put him in charge of YC.
None of these really related to Sam making a joke about Reddit. Conde Nast is extremely happy with Reddit. It's growing (#7 site in the USA), and valuable.