That could be an option but 2 issues arise:
1. Not all car rental companies allow their car to be taken off mainland, you got to check first.
2. You'll need to book car ferries for your rental car in advance to get to the Isles. The few limited slots are usually taken up quite early by locals.
Alternatively, you can take the scenic train ride up to the Highlands and rent the car on the western isles instead.
Isle of Lewis/Harris, Isle of Skye are good.
