I apologize for bringing ideas up front. Please bear with me.
A way to tackle MMR disparity temporarily (while there isn't enough activity) would be to prevent the matchmaker from sending all queued players to the same server. (The following is an overall plan for solving this particular problem)
I present you, Dynamic Capacity Servers! 
How does it work?
- By default, such a server is low capacity (6 max).
- The matchmaker prioritizes sending higher MMR players to a dynamic capacity server.
- When server is full (6 players), game starts.
- The matchmaker notifiies it when it detects a high MMR player1 in the queue. The server then increases capacity.
- If even players quit, server capacity reduces accordingly.
- Lower MMR players in queue aren't assigned to a server until all higher MMR players have joined the dynamic capacity server.
Pros:
- Prevents major MMR disparity in times of general low player activity.
- A player may still manually join such a server (MMR permitting) if there's an open slot.
- High MMR players are guaranteed to receive enough players to start a game 2.
- These servers still set a theoretical maximum for when activity picks up (i.e. 12 players)
Cons:
- High MMR players aren't guaranteed to play in a populated server unless they are lucky.
- Low MMR players might have to wait longer or cancel the wait and try another game mode / server browser.
1 Suitable to join the server as per current matchmaking rules.
2 With the same matchmaking process we have so far, see IareDave's post.
Imagine if this had been at work in the case mentioned by Nightfirebolt (opening post). As said above, the matchmaker was working as intended. But now, with the temporary measure in place, the available top MMR players would be playing against each other, and the newbie plus the rest of the earthly players would be in their own server.
(I am sorry for this is all concept and theory, and not knowing the MM internals I can't present an actual algorithm which would be of more value to the developers, but this is the best I can do.)
Edited by Hek_naw, 08 June 2015 - 11:11 PM.