So a big concern with this upcoming season is what the Pac-12 will do if teams have to play each other multiple times. There are two prohibitive favorites to win each division: Oregon in the North, USC in the South. Oregon and USC do already play each other in the regular season though, so the chances a rematch does occur to settle who wins the conference is very well in play. This might decrease overall national championship odds, particularly if a split occurs.
However, do previous conference championship game rematches end up splitting more often that not? So far, not really. There have been 17 such examples in the past, with around a 65% sweep rate.
In the SEC, there have been five sweeps and one split: 2010 (South Carolina rocked by Auburn twice), 2004 (Auburn knocked off Tennessee twice), 2003 (LSU sweeps Auburn), 2001 (LSU splits with Tennessee), 2000 (LSU sweeps Auburn), 1999 (Alabama knocks off Florida).
In the Big 12, we've had four sweeps and two splits: 2007 (Oklahoma beat Missouri both times), 2005 (Texas beat Colorado both times), 2002 (Oklahoma beat Colorado both times), 2001 (Colorado split with Texas), 2000 (Oklahoma swept Kansas State), 1999 (Nebraska split with Texas).
In the ACC, we've had two sweeps and two splits: 2011 (Clemson swept Virginia Tech), 2009 (Georgia Tech swept Clemson), 2008 & 2007 (Virginia Tech split with Boston College).
In the Big Ten, Wisconsin and Michigan State played each other twice last season, with a split occurring.
Overall? Eleven sweeps, six splits. Not too bad a percentage.
Obviously, a rematch kind of devalues the first game, and clearly since the numbers aren't 100%, the probability does go down. But in general teams tend to do pretty well upon a second glance, probably because they were better in the first place.
So yes, even though USC and Oregon might have lower national championship odds because they probably have to deal with each other twice, it's no clear death sentence. Believing that a team can't beat the same team twice is a bit of a fallacy, especially in college football. Generally, if you're good enough to beat them once, you're good enough to beat them again.