As long as you didnt go hundreds of miles with it like that then you should be fine.
With Fuse 19 pulled, the pressure plate cannot close the hydraulic clutch together and transfer drive to the viscous coupling and onto the rear wheels
Instead, all the gears inside the box spin freely. What you were hearing when you braked was the gears being released after being under strain from the different rolling radiuses of the tyres. If they cnt be put under strain (as you pulled fuse 19) then they wont thump again.
Jus keep Fuse19 pulled till you get the tyres on and you'll be fine.
If you want, there is a simple way to install a switch that can turn your 4WD on and off while on the move at any speed.
I had exactly the same probglem as you. The previous owner was running different tyres, and i was getting the thud when applying the brake. I changed the tyres last week (expensive i know!) and the thud has completley disapeared.