Sounds like a really cool project, sadly i dont have much knowledge to contribute. Still, what kind of issues have you run into? Any specific errors or problems?

I think this is a really good long term strategy, and something that is already happening to some level.

Many instances are open about blocking others, and warn eachother of bad instances (like a instance full of spam bots or bigots). I could definetly see this evolving into an alliance type network like you described.