If my sister sent me a message like this, I would drop whatever I am doing and go see her and make sure we have a final face to face talk about all this.
In short, what are the two most important commandments? Love God and your neighbors. How can you honestly say you fully live in love and give it properly if you don’t even show love to your brother. Actually, shunning is going the other way, it is taking actions NOT to demonstrate any love. It is working against love, the very thing that Jesus held as the most import thing of all.
What she is proposing is to kill the love between you two. If she truly wants to go to such extreme, she should be convinced, beyond any reasonable doubts that this is the right action to take as in the end, God will Judge people by their actions, not by their belonging to a group. And of course, all of our actions should be motivated by love. Is she convinced that such action is proper display of love?
Personally, I would not let her go easy, I would request that she explains it all to me in a very clear matter. As a last resource, I would make her reflect on the very real possibility that her kids will not stay in the truth and will end up taking contact with me. Where will she stand then?