1. Is there a way to disconnect/kill the branch circuit wires WHILE keeping the main feeder live? If so how would that be done?
2. How are the wires connected to the fuse? Connected to the fuse holder?
Just remove the fuse for the branch circuit. If it's a 2-pole (240V or similar) remove both fuses.
The wires go on a screw terminal similar to a breaker.