Are you yourself AEA, NomieRae? I can't recall...
Ultimately, the non-AEA actors don't have any protection. That's what being non-AEA means. The only power they have is to say no to the job. If you yourself aren't union, then the producer has every right to get as much work out of each of you as each of you is willing to put up with. I've seen it before, the intern company works an hour on the choreography of the final dance, after the rest of us have gone home for the night. Creating the two-tier system really ruins any chance at ensemble play, and is a real morale-buster, [unless the AEA actors are extremely protective of the ensemble, like Kristi's example above] but short of leaving the job, there's nothing you can do to keep non-union actors from getting exploited. What I would do in your shoes is to be as up front as possible with each of the non-union performers, in terms of the director's ideas of rehearsal, so that the people who don't want to put up with it just walk away from the job in plenty of time to get replacements cast.
If you yourself are union, then be very clear with the director that any rehearsal done with non-union actors will also be done without stage management. Leave it up to the director to do the scheduling, reserve the rehearsal space, clear the rehearsal space, set up whatever props the non-union actors need, and clean up when they're done. The ten-minute breaks you'll just have to ignore, but I would also ignore when one of the non-union actors then runs out of the rehearsal to go to the bathroom or get a drink of water. Now that I've typed that advice, I see that it sounds a little passive-aggressive, but I think it's just a matter of being very clear about the protections union status offers you, given that the director wants to push the envelope and would rather work without any of the rules and is probably assuming that an SM will work harder than anyone else and just get exploited along with the non-union cast.