If you're going to look at penalties per game/penalty yards per game, you also have to look at total plays per game. Logically, the more plays that occur, the more opportunities a team (either as the offensive team with the ball or defending their opponent) has to BE penalized. So logically, if a team consistently runs fewer plays than their opponent or rivals they're being statistically compared to, they will have fewer chances to be assessed a penalty over a period of time.
I looked up the total plays run/defended for SEC West teams from 2009-2012.
Total plays from scrimmage per game (average) during the last 4 years:
Arkansas 137 plays per game
Ole Miss 136
**I didn't include Texas A&M because there's only one year in the SEC to go on, but they'd probably skew toward the extremely high end coming from the Big 12 where more teams run HUNH and spread. (Same could be said for the SEC East, which has typically featured better offenses and worse defenses than the West.)
So, Alabama (on average) has as many as 13 fewer plays per game than its most distant opponent in its division, and 6 fewer per game than its nearest. If you assume a team averages one penalty every 10-15 plays or so, and teams over the course of a season are running 100-150 more plays than Alabama, wouldn't one logically expect Alabama to have 10-15 fewer penalties a year based simply on statistical odds? That's not even taking preparation/talent/luck/paying the refs into account....
But real stats don't help feed conspiracy theories, so....