It seems like what you're asking is that whenever the Doctor does something morally questionable, some other character has to actually speak up within the show and say "Doctor, you are wrong." What they're doing is far more complex because they leave it to the viewers to decide.

What the Doctor did to Harriet Jones and to the FoB *is* dark, and it's up to you to decide whether he was right. It's even possible to conclude that there's no "right" answer in those situations, just a bunch of difficult and questionable options no matter what you choose.

I don't need the show to shove its moral answers down my throat; I want it to ask interesting questions and leave them for me to think about. I think Doctor Who does an impressive job at this, especially for a supposed childrens' show.