and listening to the radio at the same time? yep that's hondas way of reminding you to not leave your keys.
if you'd like to change the beep so it doesn't do it when the key in ACC let me know, I can dig for it in the service manual. if not just throw a "push on push off" switch from radio shack in the door pin wire.
that way you can keep the door pin functionality when you want it, and can disable the beep when you want.