Divorce

As far as custody of child is concerned, the girl can be cool as generally court grants custody of child below 5 years to girl until such extra ordinary circumstances exists.

If wife wants to live with husband, she should file suit for resituation of conjugal rights under section 9 of Hindu Marriage Act against her husband. This suit will prove wife's intension to live with husband.

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File Conjugal rites petition, before court.

Since the husband left the house and wants a divorce, it is for him to initiate legal proceedings. The wife has the custody of the child and she is living in the house. So her immediate needs are met.
The custody of the minor female child will by and large continue with the mother. 

A decree for RCR can be passed  but it cannot be enforced on the husband . As husband wants to file divorce let him file for it . It will just get dismissed as there are certain grounds to obtain divorce and not such flimsy grounds . As regards to the child she can have custody and anyway he would be getting visitation rights or may be over visitation over night physcial custody . A child needs both the parents and she should not object for that . Even if she objects at any cost he would get visitation .