Since mana beans work like cocoa, I also wonder if a Forestry Multifarm setup to harvest cocoa beans would harvest and re-plant cocoa beans instead. Dump all excess beans into an AE system or sorted barrels, and you're set.
Personally, I just crucible using cheap mats, dump excess, and cleanup using cobblestone. It's crude, but effective. I only mass-crucible a few things anyway, such as Thaumium. Most crucible stuff is one or a handful at a time - not enough to worry too much about setting up an automated mana bean farm. Only so much time to spend ;-)