Running up the score really has three different levels:
1. Keeping the starters in against an inferior opponent. Example: Tim Tebow never left the game for pretty much three straight seasons. This is not a desirable thing, and I don't think CDD would do it.
2. Pulling the starters but running normal offense. Example: UTM/Memphis last year. This is fine, as it gives the backups meaningful experience running the team's standard plays.
3. Taking advantage of mistakes. Example: Ole Miss last year, USCe in 2009. Not much you can do about it when the other team keeps throwing to your defense. Pull the starters at some point, but really, don't we all just love these games? I know I do.