Its not had to get an equal split, the two destinations need to be of the same length.
Alternatively you could use 3x transposers/filters after the cobble has fed into one chest. You can also use a regulator.
You know if you really want to ban items you need to have Automatic Crafting Table and Philosphers stone banned first. Otherwise those items will still be craftable.
Thinking about it, this could actually be a positive change. With forge we may be able to do more than if we continued to use bukkit. Hell we might even get to the point where mods are automaticly downloaded and synced with a server.