If you had a Pronto remote you could experiment with slight changes to the codes frequency/timing to see if there's anything that would allow one device to work while excluding the other, but with the Harmony there's not a whole lot else you can do in the tweaking department.

The only real way to stop it from responding to codes that it shouldn't be responding to, is to prevent it from receiving those codes in the first place.

You could try to block its IR receiver as much as possible so that it can only barely receive a command when the remote is aimed directly at it...