To answer your first question, I would be hesitant to say that there was a single leader as part of the conspiracy. While it wasn't solely concocted by the Pazzi family, they had of course a major role in the operation due to their own conflict with the Medici. Although if leaders had to be identified, I would cite Francesco Salviati as the main one, followed by both Francesco and Jacopo de Pazzi. But as I have said, there are numerous other players involved, such as Pope Sixtus IV, for example.
As for Assassin's Creed II, it has been a good few years since I've played the game, but I'll look up a list and label them as real or not real. If you want any expansion on them or your first question then just let me know and hopefully I can provide. To further preface, there was no Auditore da Firenze family.
Leonardo da Vinci - real
Rodrigo Borgia - real, served as Pope Alexander VI
Paola - fiction
Antonio de Magianis - fiction
Rosa - fiction
Uberto Alberti - fiction, although the Alberti were a major Florentine family and allies to the Medici
Carlo Grimaldi - fiction, although the Grimaldi are a major dynasty and the current Monaco royalty are members of the House
Lorenzo de Medici - real
Giuliano de Medici - real
Bartolomeo d'Alviano - real
Jacopo de Pazzi - real
Marco Barbarigo - real
Silvio Barbarigo - fiction
La Volpe - fiction
Vieri de Pazzi - fiction
Francesco de Pazzi - real
Checco Orsi - fiction
Teodora Contanto - fiction
Caterina Sforza - real
Niccolò Machiavelli - real
Antonio Maffei - real
Cristina Vespucci - fiction