Set low priority. In linux start the litecoin miner with "nice":
screen nice ./your_lite_coin_script
(Screen is optional; it lets you attach and detach console sessions)
IN windows open task manager and set process priority to lowest.
Yes, I have considered this, but haven't messed with it just yet. I drop the priority for the dedicated cores I put to it, but haven't messed with running both a GPU and a CPU associated with the same core with the minerd at lower priority.
I may fiddle with it eventually, but it's only 6 cores that I have right now. Not too much I'm leaving on the table given CPU chain value ATM.