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.