Could you modify the powder measuring system? That would be the first way I'd think of doing it, preload a charge either based on weight, or in a transparent tube with optical sensors, then dump the pre-metered charge into the cartridge. That way you don't have to worry about dealing with the brass at all, you can make your own system as simple or complex as you need to. If the metered charge doesn't fill properly, or you detect powder still in the metering system after a cycle you can flag the round for inspection.
Is it reasonable to assume that each cartridge would be empty as it goes into the filling station? I would think that the process of replacing the primer would keep any already-filled cartridges from going thru, but I'm just guessing.