Racism and discrimination have been ingrained into the very fabric of society for thousands of years and it still pervades to this day (things are "better" but it does not mean they are "fixed"). I don't think simply putting good and evil people on both sides of the war will make it okay to use one group or another as cannon fodder for the protagonist. Just so long as there aren't any average shmoes who are mustache-twirling evil (aside from the main villain because that's how they are in these games) simply because they are working for the bad guy. People are more complex than that. One of the mechanics I've always liked is that after murdering several enemies in a row sometimes the remaining combatants will just give up and run away even though they are honor-bound to fight to the death. It shows that their allegiance is to their paycheck, not the banner under which they fight.
Ezio was a wonderful protagonist because he wasn't necessarily a "good guy". He had noble intentions but the methods by which he achieved his goals weren't always morally sound. "Everything is permitted," after all. The guy is, in fact, a mass murderer. Certainly he had a very personal reason for killing the people he did (sweet sweet vengeance) and he made a concerted effort not to kill innocents (...minstrels don't count). However, some Templars he murdered did actually have noble traits and died continuing to believe that they were doing the right thing (and in some instances Ezio even AGREES with them), but he kills them anyways because they happened to be on the wrong side of the conflict.
Ezio was a wonderful protagonist because he wasn't necessarily a "good guy". He had noble intentions but the methods by which he achieved his goals weren't always morally sound. "Everything is permitted," after all. The guy is, in fact, a mass murderer. Certainly he had a very personal reason for killing the people he did (sweet sweet vengeance) and he made a concerted effort not to kill innocents (...minstrels don't count). However, some Templars he murdered did actually have noble traits and died continuing to believe that they were doing the right thing (and in some instances Ezio even AGREES with them), but he kills them anyways because they happened to be on the wrong side of the conflict.