I was editing my post several times, sorry, maybe you already answered before the final editing, just wanted to point that out (if you want to refer to some other things in the post^^).
As far as my experience tells me (i too was part of a rather small Private-ClassicWoW-Project), any diversification of player-rights leaves the Server-Team open to really problematic criticism, that can damage the reputation of the Server beyond repair. Of course this "little change" may have rather small impact (don't know for sure), but its rather the impulse, that comes with it. If you overstep the line once, next time won't be as hard to do as the first time^^.
So no, even though it might somewhat reasonable, i absolutely can't get behind such a system.
I also want to avoid a long queue-system of 30mins or more, because this would exactly lead to the things you described. It's a delicate matter to introduce a queue. But there are possibilities to get the benefits from a queue-system (stop population growth) without producing too much wait time (my assumption, can be contested!), the Team therefore needs to find the right number for a queue and also handle it somewhat dynamic.
This would be, if there would be no new server. If a new server is introduced, a rather harsh cap could make sense as stated above.
But why is it unlikely, that a whole guild transfers to the new Server? I'm just curious - what are the really big downsides? As far as i remember my own social contacts always centered around my guild anyways.