For the most part yes, you'll be fine. As long as a character isn't linked to a village and known to be your hire, there are no consequences. However, the spirits frown upon such behavior. Once you've killed enough innocents, you'll receive a message warning you of the sense of unease you experience. This sense of unease is a very real negative luck effect on your future endeavors, designed to karmically punish you for your murderous ways. Njerps don't count.