Tough situation OP. When is your wedding? If it is not for a while I'm going to buck the trend and say don't talk it over with your brother. He sounds like he has enough on his plate without concerning him with your wedding party (sorry if that sounds harsh.)
See how it pans out with their relationship. If they kiss and make up you may feel uncomfortable having given out about his wife to him and having sacked her as MOH. I'd ride it out and say nothing for the minute. If they are still on the outs closer to the wedding then maybe talk to her and see if she feels comfortable proceeding or if she would prefer to resign. Really awkward one, I don't envy you at all, particularly as she will always be the mother of your nieces and nephews.
Would agree with Hbombadero. Might be wise to sit your ground for now and avoid risking another conflict amid high tensions. It's understandable that it's hard to witness what you see as poor treatment of your brother but interventions - inadvertent or otherwise - might not be best. Hopefully they'll work it through.
I would keep stum too. Do nothing for the time being. It really is your brother's life that he needs to sort himself. You might be surprised that sacking her as MOH may not please your brother as you imagine. Definitely refrain from slagging her off even though you might feel like it. Listen to your brother and be there for him but make no criticism of herself. They end up getting back together as thick as thieves and there you are awkward as you like with your brother knowing what you think of her. Then he tells wifey and bingo-you're the baddie ! I've seen it happen with friends- couple break up and everyone sees it as free for all to criticize the ex-partner. Either friends gets very defensive( eh! I went out with this person- hold on! they are not that bad!) or else couple get back together and sometimes too much was said to continue seeing certain friends....With family, you need to be really careful about what you say about their partners- as our choice of partners reflects on ourselves too.