I am giving you huge kudos here for wanting to try to have a relationship with MIL again. I don't think you can set any boundaries with her, without sounding like a witch because she crosses lines that are obvious to a rational person. I think you and DH will have to take a firm stand with her. First, like Sassy said, your DH needs to set his own boundaries. He can't call and rant to MIL every time you two have a disagreement. That is just setting you up. No, MIL shouldn't call and yell at you, but DH shouldn't have called her to begin with. There's a huge difference in looking to a parent for some wisdom and looking for someone to side with you.
Second, I wouldn't try to sugar coat it. You can say what you mean, without being harsh, but it needs to be clear-cut. I remember telling my DC plenty of times growing up, "I love you but that behavior is not acceptable." I wouldn't even dwindle down to details, just set some all-encompassing rules.
1. Our personal life, is our personal life. Discussing our religious choices, birth control methods or anything to do with how we chose to parent, is off limits. You got to make your choices in life, we would like to make ours.
2. There will be fair treatment of our children. That is not up for discussion. They are children and do not understand when you treat them differently. We treat them equally and expect everyone else to as well.
3. You have made it clear that you don't agree with how we handle DD. We get that. How we choose to deal with DD's medical, social and schooling is our choice and not up for discussion as we know you don't agree with how we are doing it.
That is what we are asking for. We want you to part of our lives, but not dictate how we live our lives. We may make mistakes, but they are ours to deal with.
She will have a choice to make. She can either live with these rules, and honestly, nothing you are asking for to me is outside of what everyone should want or expect. Scoop is right about you having to keep reinforcing them if she agrees to them. She's gotten used to being a certain way with both of you and is not going to change overnight. I think you will have to repeat a few times, "That was one of things we discussed that was off limits" and be understanding if you see her trying, but she slips up. Bad habits can be broken, but sometimes you fall off the wagon a few times.