This could work. However, I would make any type of automating items not be purchasable at all, and only be drops from regular world gen mobs. This means that even people who try to make mob farms using the bee effects (zombie spawner, creeper spawner, etc) would not be able to farm automation related items.
So regular mobs in the world would drop the following items at a ridiculously low rate:
1) Buildcraft pipes, including apiarist pipe.
2) Autarchic gates (only the basic lowest).
3) Factorization Router and all upgrades (excluding the bugger thoroughness upgrade).
4) Any other automated stuff I'm missing.
The rest can be purchased. This forces players to work together to go on "mob raids" and split their loot evenly, etc. Finally, I would disable the production of alvearies as they can very quickly disintegrate your server economy. The scarcity of bees + apiaries will keep the server going for a while. Frames can be bought for cheap, but only because apiaries exist in this server, it doesn't matter, since they cannot be auto-inserted via routers, etc. So only "hard-working players" who are tending to their apiaries can reap the rewards.
Banned items:
1) Anything that provides chunkloading. Chunkloading makes bees OP beyond belief.
Lastly, if you ever have this server up and running, please let me know. I love bees to death and would play this server.
EDIT: To explain my point about not allowing alvearies: Minecraft is a game where a stack of items only go as high a 64 (and a small inventory to boot). This is a small number, and by allowing alvearies, you'll very quickly be dealing with currencies at a larger scale as opposed to alvearies when coding your transactions of trading combs for stuff. It is always easier to work with smaller numbers as opposed to larger numbers (which are unnecessary, IMHO). For example, think of MMOs where items are sold for stupendous prices (e.g., one eq for 500 million of the game currency).