Regarding the brother, I would keep doing what you have been doing now. Try for the two of them to have a good relationship as much as you can. If the mom is non cooperative , there is not much you can do but at least you can be sure you tried your best. When she grows up, you can honestly tell her that you did your best, otherwise she might resent you.
I also don't think it would get too confusing for her. Maybe for us because we have a prejudice and see things differently but she will understand that she has a brother even though their relationship will be different.