I've never done this but, if I left Helgen with Ralof and sided with the Stormcloaks and did the Jagged Crown quest but gave it to the Imperials will Ralof disappear from the game or stay in Riverwood?

I did the opposite - followed Hadvar from Helgen, did the Jagged Crown for the Legion, and then gave the crown to Ulfric. Haven't seen Hadvar since, but Ralof has shown up instead.

So to answer your question: he will disappear from the game.

So is Ralof and Hadvar the only npc that can reversed-pickpocket with the Jagged Crown?