Shrema, It strikes me that your mortgage banker does not want to resubmit the application for you. What you would like to do should be possible, as far as I know, and yes,, it does reduce the commission on the loan. You might try telling the mortgage banker that you've found someone who is competitive on rates and will sumbit your application with the additional down payment. My gut call will be that he/she will come around quickly.
Good Luck, Todd Norsted