I think they are just jerks, frankly. But perhaps there is something far more sinister afoot!
The footpads from Morrowind Comes Alive spawn very frequently in towns, and create just one more source of imbalance for a few different reasons.
1) Low level characters can often be killed in one or two hits by the footpads, but can't try to strike first, because it might be counted as a crime. At least, that has happened to me. Furthermore, guards won't help until you're hit at least once... which might be your death. Cue reload and frustration.
2) If you do survive the attack, and the corpses lie there for you to loot, one can get a moderate amount of free gold. True, you don't have to loot, but things are so much better when balanced by design rather than balanced by the player's will. This is an issue across the board with Morrowind, and made worse by a lot of awesome mods, but you do what you can ^_^
3) Not so much "imbalance," but even at high levels when you'll swat the footpads like flies... the attacks can just become simply annoying. Why don't those guards just do their job and keep the peace so you can walk around towns freely, huh? It gets old. But I can appreciate the sentiment of why it was included in the first place. Personally, while I enjoy MCA, I've been phasing over to Starfire's NPC mod and am hoping she'll one day release the addon for guard patrols and such with NPC vs NPC combat to make the world more alive in a less player-centric way.
Until then, though, there is http://planetelderscrolls.gamespy.com/View.php?view=Mods.Detail&id=6804 patch for MCA 5.2 which removes footpads from towns. If you tire of the footpads as quickly as I did, you'll soon need it =).