That's the right way to do it as riX says. The software can generate a new bitcoin address whenever you need one for each payment. "Please send X bc to [single-use bitcoin address] to complete your order" When the server receives that amount to the bitcoin address, that could trigger it to automatically fulfil the order or e-mail the shop owner.
Adding command line support is a high priority. It's just a matter of getting the time to code it.