Should a Beit Din take away the children from their Mother ?

B"H

Today, I met Sarah Einfeld (she left Chassidut Gur) and the following question arose:

Should a Beit Din, no matter if the Rabbanut (Chief Rabbinate) or the one in a chassidic group, take away the children from their mother ?

Lets say, a mother with children decides to leave a certain haredi direction (chassidic group, haredi society) and becomes secular. Because she does not keep Shabbat anymore, the Rabbis seem to have the right to take the children away from their mother and hand them over to the father. Is this fair ? Especially in a case where a husband abused his wife ?

One response I got was that the mother can ruin her own spiritual life but does not have the right doing the same to her children. Therefore, the children should stay with the father. On the other hand, a compromise should be made. The kids should be at least on Shabbat with the father, if not during the week.

Anyone has a further opinion on this difficult subject ?