You can just cut out the wood and remove it. Unless the frame is seriously compromised, nothing will happen. If you replace the wood and correctly fasten it to the frame and the shell, you will have a box and it will be plenty strong. Where this design falls down is that it depends on the plywood as the joining medium between the frame and shell and when the wood rots, the box structure and stiffness is gone.
Here is a thread with my progress on replacing the floor in my 73 Overlander: