I started watching Agents of Shield about a month ago, and my perception is that the things that make a lot of viewers uncomfortable are quite intentional. It seems like they spent a lot of time in the early seasons shoving the parallels between SHIELD and HYDRA in viewers faces, and they've been consistent all the way along about presenting most SHIELD agents as uncritically accepting their actions as necessarily good for no reason other than that they are the good guys acting upon bad guys. Hell, the agents on Criminal Minds feel more empathetic toward serial killers than SHIELD agents feel toward most people who aren't them if they see those people as being in their way.

Of course, I have to admit that I also used to occasionally suspect Stargate: Atlantis writers of knowing what they were doing, and that turned out not to be the case, so it's perfectly possible the AoS writers really think they're doing a helluva good job of representing made-for-TV heroism.