For starters, if the hotel has a better suite than the one that was confirmed in your reservation, they should have offered it to you at no additional charge. This should have been done automatically.

I would be very suspicious about how the manager adjusted your rate. You should not pay any more than it would have cost you on the day you made your reservation if you had booked the junior suite at the best rate for which you were eligible.

This hotel needs to understand that a reservation is not an "option" for them to give you the room you have booked at the stated price if they can't sell it to someone else. Presumably you booked the room type you want and if it were not available, you would have selected a different hotel.

Have you asked about being walked to an equivlanet (not necessarily Marriott) hotel that does have a suitable senior one bedroom suite amiable for your stay?