In general I would advocate for staying in the place you are flying out of the night before for any early flight. Siena to Florence is manageable but there is always the possibility of strikes, road or rail works or other things you can't control. What is your back-up plan when the way you were going to go isn't working?
The most direct way to Pisa is a train about 1:45-2:00 hours usually changing in Empoli. There is a 5:00am arriving at 7:32 and a faster 6:25am arriving at 7:51. The airport in Florence is close to the train station and there is a tram.
https://www.trenitalia.com/en.html (use Italian names for cities - Firenze for Florence for best results)
The station list for the 131R is here: https://www.at-bus.it/en/linee-e-orari/regionali-131r the FIRENZE AUTOSTAZIONE stop is near the train station and the tram for the airport.
Hope that helps,
=Tod