I'm sure neither was intentional, but that doesn't mean anything. That anyone subconciously makes these equasions does not make me comfortable on any level.
I didn't pick up on the 'killing helpless prisoners', but you are very right about the main character. The probably with Mal was that you could feel how hard the writers wanted you to like him, which made him even more irritating than Jayne, who yes, was worse, but was called on his actions. Mal never was.