"charge controller has an internal short"
Look at the internals of most CCs. Would anything shorting out inside of them be enough to blow that size fuse?
Make sure everything around it won't join in to the smoking.
"the wire to/from the scc has a short."
Obviously this can not be ruled out, However, the risks can be minimised to such an extent that they are lower than the risks associated with the proposed fuse solution...as you have found out.
Sometimes our solutions create bigger, more likely problems!
So the CC is already cactus from the PV side? ...not much for the fuse to do in saving the CC.
Fires can still start on much lower amperage than what can usually pass through most of the fuses installed between B and CC.