Setting the config line for the furnace cart recipe to true disables it, while leaving it false enables it. Tested in Railcraft 9.6.1.0.

I believe I've located the bug at:
ModuleCore line 191
Condition needs to be inverted.

Of course the default value would need to be changed at:
RailcraftConfig line 320

However this would likely cause issues with people loading from previous configs. Thus it would likely be simpler to change the config description.