There is no bar in letting out the property.
There are many ways, and you shoud commence negotiating with the unwilling banker and convince them to strike for a deal. Even they can propose a deal if you are prepared to close the entire loan in one lumpsum before a stipulated period.
As far as I know you can not have the cake and it too. The bank employees are not dumb. They have got their own external agents / engineers who has to periodically report a market value. They have not been bringing pressures because RBI was previously not that much strict, and as the property value is more. Though you are giving your own estimate, one can be sure it costs minimum of 5o lakhs. Catch hold of a good client of theirs and commence negotiaing. Please remember you have paid interest because you have used. Just imagine how much you have benefitted by the loan, and value of the money when you have taken and present value. You have paid the interest because you have used the principal. Because you have delayed you are still paying. The maximum concession they can offer is waiving penal rate and compound interest and it may come around Rs.5 lakhs in total. They may afford to sacrifice that much and not more. (The interest rate they are charging is nominal for educational loans)