Being the good guy seems the better choice overall imo. While you might earn less money, you get discounts in the shops, have access to better items (some clothing is unavailable unless you have high enough honor), and sometimes you get the chance to buy any one item for free from a shop after helping someone in a random encounter (in my case so far i can buy a free weapon at the Valentine gunsmith, but i'm waiting to unlock the better weapons before using the discount).