You could try to argue ignorance with the MR desk or ask the desk folks to add your MR number to the night to get credit. Unless the deal on Hotwire was just that much better, you are probably safer using the MR site in the future though :)
actually i think we should start to question marriott rewards that they look into giving some credit for these and other 3rd party bookings since this can really be the wave of the future in saving money on hotel stays. I think if enough of us ask it could become a reality. I can remember the times when internet was always a charge and so were 800 calls. Things can and do change.