empyle is right--though I don't have DirecTV either, I do have both digital cable and regular cable connected to my 5160. You can delete the DirecTV channels that are duplicates from your Replays channel guide (from the setup menu). The regular cable channels should be found at 1000+. The 1000+ channels are only a little inconvenient (mostly just difficult to explain to other family members).
After deleting the channels, you won't see those channels in the Replay channel guide at all, and they won't be picked for theme recordings. You can still, however, direct tune to them with the number pad on the replay remote.
My wishlist for new features would be channel maps for theme recordings (mostly I'd settle for just one global exclude map I could choose or not, but more flexibility would be better. For some recordings, just being able to choose to limit the theme to just one channel would do it for me.
Hope this helps,
-se