I thought of something similar:
1. use vanitygen to make a few thousand addresses offline.
2. use pywallet to make a watch-only clone wallet.dat. Then you can use bitcoind safely.
3. use something that notifies you when 50% of the addresses have been used. You then manually add new addresses. Or you keep track of your orders anyway, so you should know.
I read somewhere that you can generate a 'seed' for public and private addresses offline and then use this public seed to generate as many addresses as you want on your public server, i.e. one per customer. Any time funds are spent to these addresses they are then in cold storage. Using the private seed, which you store offline, you can then access any of these cold storage addresses when you want.
I can think of a couple ways this can be done cryptographically. I can't remember specifically where I first read about this but I've been meaning to read/think more on this at some point...
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