Red is working for an Evil Empire, while Blue is employed by La Résistance
It's quite obvious which side is supposed to be the good guys. Red's objective on one map is to literally kill captive peasants, while Blue has to rescue them. Red's name, the Iron Company, is much more ominous sounding than Free Guard of Blue. There's also the fact that most maps are severely skewed in Red's favor at release, which would make perfect sense if Red is the one receiving the backing of an empire while Blue has to make do with what they have.- It might just be a case of Deliberate Values Dissonance. During the Middle Ages, there were basically no protections for noncombatants; Rape, Pillage, and Burn was standard practice for pretty much all armies, and civilian deaths were simply an expected consequence of warfare. It might make more sense to think of it in terms of Defender/Attacker instead of Good/Evil. They are mercenaries, after all.
If samurai weapons/armor are ever added to the game along with the Knight and Viking weapons/armor...
A new taunt will be added in the same vein as "And they say Chivalry's dead!." Namely, something like "Does no one in this land fight For Honor?!"