i would investigate if you can put MDS 9124 into NPV mode (that will wipe its' config) and if DS-300 support NPIV. This way MDS 9124 will essentially become a "pass-through" device and you would not have to mess with interop.
You may be able to create a VSAN on the cisco with the ports you want to connect to the Brocade. Put that VSAN into inter-op mode. Connect the Cisco to the Brocade and they "should" link up. You would have to do inter-vsan routing to zone anything on the brocade to the cisco and vice versa.