Stresa would be my choice also. I’ve done it only by car and the drive is about 45 minutes. If however your flight is super early in the morning, I don’t know if it would be doable with public transportation. There is the SAFduemila Alibus which connects Stresa to the airport in about one hour, but not sure if the first bus can get you in time to MXP for a very early departure. The alternative is the train from Stresa to Gallarate (35 min) then from the Gallarate station you can take a city bus or the taxi. In the early days (prior to 2000) before they opened the new Malpensa airport with the Malpensa Express train from Milan, I used to stay overnight in Gallarate before my flight out of MXP. The taxi ride from the station was about 15 min. In those days they also had an express bus from the Gallarate station to the airport which would take you to the airport in just 25 min. I don’t know if that bus still operates nowadays. There is also a city bus but makes too many stops. The train plus taxi can easily get you at the airport by 06:20. The first Alibus can get you there by 7:30.
PS: “Ali” means wings in Italian. Hence the name associated with anything flying, like Alibus or Alitalia. Nothing to do with Mohammed Ali or some other middle eastern name.