Maybe the solution is more on the client side. An app should be able to let the user add communities from different instances and present them as one, maybe even merge comments from identical posts etc. Then if the user gets fed up with some instance not moderating or spamming, the user could then just remove that from his multi list.
Technically there’s no way to please everyone on this, but there’s also no reason why the apps couldn’t present a meta-view of what is actually happening across instances, if that’s what the user prefers. Most users don’t want to see the gears turn.
In addition to the user experience it would also minimize any “damages” from any instance going down, because the multi list would remain active as long as any of the instances are up.