Honor and duty are essentially a separate axis from good/evil. Killing a sentient being is never, in and of itself, a cruel or evil act; it is, at best, neutral. You have to look towards the cause of, and the execution of, the act in question. Was there a relationship between the two individuals?
In the first case, the rogue stole money from the samurai. Likely, honor dictated that the rogue repay the debt, and if he could not, his life would be forfeit. In this instance, if the samurai killed the rogue when the latter failed to repay the debt, then the debt would be considered repaid, the honor of the samurai would be restored, and that would be the end of it.
Now, if the samurai then proceeded to hack the rogue to death, murder his whole family, etc, etc, then it would be considered an evil act (the mutilation of the enemy and the destruction of the rogue's family). Now, a good samurai might have looked into the man and found some part of him redeemable, accepted a term of service as an acceptable payment, and sought to transform the rogue into an honorable man. At best, your samurai player character in question is "honorable neutral."