Ownership on property purchase and coapplicant are two different things. All the above matter is subjected to mutually understanding and relation of coowners.
If your mother agreed to transfer his share of ownership to u both u have some options left with urselves:
Either u can make the gift deed whih you have to get properly registered through registrar with the nominal value aprox 20000 rs.
You can also execute release deed,sale deed, transfer deed in the name of beneficiaries from ur mother side.
It is not necessary that she has to remove from coapplicant from the loan.
I will suggest you to go for transfer application as it will consume less time and money.