Mother name different in kids passport

Dear Sir Iam RAJUCHAMBANNA VEERABHDRAPPA YARADAL having a valid Indian Passport applied from Bangalore Passport office. I also have my spouse passport with her maiden name as PRATIBHA KHODANAPUR and have not changed after marriage. I have my child passport with her mothers name as PRATIBHA RAJUCHAMBANNA YARADAL instead of PRATIBHA KHODANAPUR. Now I have approached the Registrar of Birth Certificate for change of mothers name as PRATIBHA KHODANAPUR instead of PRATIBHA RAJUCHAMBANNA YARADAL. But they say that it can be done only after Courts order. Other option what they have told is that they can re issue Birth Certificate with mothers name simply as PRATIBHA without any surname. With above explanation, is it ok to have such arrangements. Is there any issues in future. Or what is the best solution to avoid any discrepancies for a safe journey. Pls help