Regarding Spock and ethics, I felt that his mind-touch with a grieving Kirk at the end of 'Requiem for Methuselah' was questionable. Spock did not ask permission to initiate this contact, which is highly unusual for him with people he knows.
This is the only one I'd call debatable.
As for the others, following rules and regulations has little to do with morality. There was nothing wrong with wanting to defend himself/Kirk/the miners against the Horta before he realized its true intentions. And I can't believe people are actually serious about the Romulan Commander thing.