You would have to refer to the scanner documentation. Even though I have no experience with such devices, I would imagine that such a device hooked up to a keyboard port is essentially acting as a automatic keyboard. When you scan a code, the scanner is just emitting "key strokes" as if you entered them on the keyboard yourself. Therefore, I would suspect that you won't be able to block manual entry because the computer doesn't know that the device hooked up is a scanner versus a regular manual keyboard.
Again, this is just based on an assumption of how such a device is likely to work. You'll have to read the manual to find out for sure.
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Peter