In Scorched Earth, I thought it was more that she was following his orders as a commanding officer, but it's been a while since I saw the episode, so I could be misremembering. In general, though, I think Sam's suffered a lot of character assassination for the benefit of the Sam/Jack plotline, which is sad because I really like her some of the time.

But she knew that Jack's commanding officer was against the idea. In the CoC, general trumps colonel. Her loyalty to Jack was stronger than both her moral viewpoint and her loyalty to the Air Force. I just... relaly hate that scene. And yeah, Sam's suffered a lot for the storyline, which a large part of why I hate the storyline -- it makes Sam a weaker character.

Hasn't Jack ever been compromised by his feelings, whatever they happen to be, for Sam? There's the big example of Upgrades, and I could've sworn there were others. He doesn't cross the line as much as Sam seems to, but he doesn't always manage to walk it perfectly.

When did he cross a line in Upgrades? He stayed for her, and Daniel and Teal'c stayed for them. Jack was not the only person there ready to die rather than lose a teammate. They all care 'more than they should'.