The BCS compliant version does not use MOV at all. There is no distinction between a 21-20 nailbiter, and a 63-0 blowout.
The main version does consider scoring margin, but its effect is diminished as the game becomes a blowout. The score of each game is translated into a number between 0 and 1. For example 30-29 might give 0.5270, while 45-21 gives 0.9433 and 56-3 gives around 0.9998
The maximum is topped at 1, so the curve flattens out for blowout scores. In addition, I do a Bayesian correction to reward each winner, regardless of the game's score.
The net effect is that there is no incentive to run up the score. However, a "comfortable" margin (say 10 points) is preferred to a narrow margin (say 3 points).
In summary, winning games against quality competition overshadows blowout scores against inferior opponents. Each week, the results from the entire season are re-evaluated based on the latest results. Consistent winners are rewarded, and a blowout score has only marginal effect on a team's rating.