If you're having trouble having your "good" characters accept certain missions, you could try a line of reasoning that I sometimes use for my characters, which is: "This lord is going to get someone to do this eventually, better to do it myself so I know it will be handled carefully and morally."
For example, the murdering a merchant quest. Your character could accept with no intention of following through, sure you may get into a scuffle with the guy but in the end he'll know that the powers that be have it in for him, but he'll still be alive. Or raiding caravans, your good character will tell his soldiers to engage with blunt weapons, and release the captured caravaners afterwards, if you turn down the mission some bloodthirsty mercenary may get hired to do the same deed and go forth causing a lot more suffering. In this way a character can balance duty to country with duty to self. Can it be harder? surely, but it is doable. Hope this helps!