My thought is that perhaps the Jedi don't need any sort of formal organization. That all of them following the Force automatically brings them in alignment.
In my outline for Ep. II, there's a Jedi Conclave, where perhaps 300 Jedi from across the galaxy meet to discuss the Clone Wars, and celebrate one Jedi's acheivement of High Master (achievement, not promotion, as there's no formal organization).
The New High Master (Jedi Thorpe) renounces his status as a warrior, and goes to live a monastic life. This hints at Yoda's existence (and perhaps he gets a name drop), as well as makesa good 'what a bastard' moment when Anakin sells this dude out, giving his location to Palpatine for assasination in Ep. III.