As a former TA, you should have no problem finding one who will book you two separate components of your vacation. Why wouldn't they want to book you in whatever hotel you wished? You will just need to be specific that you do not want the "land/sea" package that is offered by Disney,and that you do not want a Disney property. There are hundreds (of not thousands) of lodging options in the Orlando area. If their concern is over the transportation, you can certainly book a town car for your own transfers quite easily and leave out that component altogether. Since you will be staying quite a long time, you may want to consider having your agent book you a rental car with Budget or one of the other companies offering a location near Port Canaveral. That way you could arrive in Orlando, rent your car, go to your villa/condo/hotel (whatever your lodging preference is), and when you check out, you could drive directly to the rental location at Cape Canaveral, drop off your car, and take the complimentary shuttle to the ship. After your cruise, you could take the Disney transfers one way back to the airport if you will be flying home the same day.
I have a feeling that the agents you have spoken with do not want to be bothered (or do not know how) to book a property other than Disney. It may take them more time and effort, but they should be able to do what you wish.
Good luck!
