It might be too late to change the rules about this in the game, but I always found the systems with only one metric for Reputation clumsy. As shown by the preview, you lose reputation when you do something wrong and you gain it when you act positively. Isn't it nicer to have two metrics for reputation: Fame and Infamy?
You would still gain fame when doing something cool and lose it when doing something wrong. But you would conversely gain and lose infamy in a symmetrical way. That way, you could count your reputation with factions/NPC which have no ethics (or ethics really different from ours) and still see how famous you are with all the cool people... Just my two cents.