Caesar is actually described as having a "neutral" karma. He doesn't think he is evil, since people he gets killed are all barbarians anyway. Let's say he just favor order above all.
I mean, sure, the legion is portrayed as the bad guys and the game don't give you that many occasions to get to know them, but if you search for some lore about Caesar, the legion can look like a valid option without playing an evil/bad karma character, just like any other faction.
Also, Nipton had it coming anyway.