The courts while dealing with these types of cases often prioritize the welfare of the child and the situation’s best interest. You in your query have stated that your parents are legally separated, which automatically denies the fact that your dad can live in your mom’s house forcefully without her consent. Therefore, the court cannot order to let your father stay with you all, although he can be given some visitation rights to meet you and your sibling.
The Domestic Violence Act, 2005 safeguards the women’s residential rights after separation. Therefore, if your mom fears harassment or violence from your father, she can seek legal protection under the act. The case of SR Batra vs. Taruna Batra laid emphasis on the importance of the woman’s right to live peacefully in her matrimonial home. The court in the case held that a husband can’t force himself into the matrimonial home against the wife’s wishes.
But before taking help of the legislations or dwelling into legal proceedings, it is recommended to first sort the dispute through mediation and if the amicable efforts doesn’t work out, you may approach the court along with all the necessary documents which prove the separation of your father and mother. You can also refer to the Hindu Marriage Act, 1955 for more details.