If you retain your ISRCs and UPCs when moving from one distributor to another, links and stream counts will remain as is.
Surely that's an issue solved by the market, if there is a distributor that is reliable & fairly priced then people will move to use and stay with them. I think the current issue is that a lot of the big name distributors are marketers first, distributors second.
Since when are non-profits not part of the market?
No commercial distributor can hold out forever against the temptation expanding into marketing. That's as hopeless as wishing that ISPs would stay as dumb pipes.
There should be more competition: a non-profit which offers fewer features but which you aren't constantly wondering when it will flip and screw you over, versus more featureful and slicker commercial competition.
They're not, but I don't see how it being non-profit would make a difference to the problems you're suggesting. You can be for-profit and still have a sustainable, fair and innovative model.
By marketing I mean marketing themselves as a service, not marketing the music they handle.