When I first started going to SEC home games at Auburn, I noticed the same thing. Even during the Iron Bowl against Alabama, when whichever team hosted the game could expect at best a 70-30% attendance advantage, it was passionate but generally civilized. I think you're right that it's the expectation of more professional sport fanbase type behavior that caused the surprise, what with Sox/Yankees, the city of Philly, etc.
The were two exceptions to the rule of surprisingly civilized fan behavior that I noticed back when I went to SEC games frequently (1999-2010, more or less):
1) Near the visiting students' section, since you're likely to have the less mature, drunker, most die-hard fans from the school. Since they're usually concentrated into a single section, I think you're unlikely to encounter enough of them as a general rule for it to impact the fan experience, unless:
2) LSU. This is by no means an exhaustive survey, but one of the few things Auburn and Alabama fans agreed on when I was around was that LSU fans are the closest thing to a barbarian horde in terms of fan behavior. Vandalism on campus when they would come visit, they'd actually light the occasional rally van/truck/car on fire when they hosted, and in one case were said to have thrown bricks at some of the opposing team's band members outside of the stadium. Hard to say what's legend vs reality here.