There are probably better solutions but I guess simplest way would be to solve that at the client end?

Give users the option to merge community views from different instances (maybe too much hassle for the average user), have the client do it automatically for some specified communities, or have a mechanism by which the communities can hint the client to merge their content with specific "friend" communities.

From users POV the last option would be the easiest (but it should be possible to opt out of it or customize the behaviour). To prevent trolling and harassment the merging would require an authentication from all participating communities. That doesn't prevent multiple posts on the same subject but if majority of users see the same combined content the likelihood of double posts decreases. It would still spread the load between instances, and if they want the different instances could specialize on different aspects of the subject.

Just a thought. I don't know if it makes any sense from technical point, maybe it would be easy to implement without any changes on the underlying protocols or maybe it would require some ugly kludges and would just overcomplicate everything or is something not many people would even need or want.