Bonanno wasn´t planning to kill Gambino and Lucchese. The accusation against him started when a Profaci member (allegedly Joe Colombo) noticed Bonanno´s son, Bill, staying in Magliocco´s house at the time when Magliocco was prepering for war. Bill was having marital problems and his wife was Magliocco´s niece (I believe). The missunderstanding of Bonanno´s involvement in Magliocco´s plot was sorted out during a meeting between Bill and Gambino/Lucchese.

The distrust between Bonanno and his cousin, Stefano Magaddino (a Commission member), was actually the underlying problem in what was to come. The distrust went so far Magaddino accused Bonanno for "planting flags all over the world" and Bonanno suspecting Magaddino of secretly trying to plot his demise by installing DiGregorio as boss of the Bonanno Family. If you are interested in the details of this, they can be found in Bonanno´s memoirs. Nothing else but the mistrust between the two cousins was THE fundalmental reason of the "Bananas war". Magaddino initially had tried to use the Commission to dispose of Bonanno. Gambino and Lucchese on the other hand (and they had their own agenda of dismantling the conservative faction´s power on the Commission) used Magaddino for their purposes by rubbing him the right way. And all the time by staying in the background. For many reasons, they certainly weren´t keen on the idea of going to war at that time.

Joseph Bonanno´s move to Arizona was a part of a peace treaty after the "Bananas war". So he wasn´t "kicked out" in 1968.