Is saying: "Why does it scold you? It's from the same food they'll cook for you tomorrow," when a friend talks about stealing fruits from the free university restaurant, considered permitting theft and necessitating apostasy?

Your friend's action is not a deeming permissible of theft or a mockery of religion, because it is her interpretation that what she took is not theft, given that the restaurant is free and what she took is from what the restaurant gives for free. Deeming a sin permissible occurs by believing it to be lawful, and the place for excommunication due to it is if the forbidden act is unanimously agreed upon as forbidden and its ruling is clear among Muslims without interpretation or doubt. Your belief in the prohibition of theft means that you do not deem it permissible. Beware of obsessive whispers (waswasa) and turn away from them, for they are from Satan and increase with indulgence in them. Seek refuge in Allah from them.