The whole "doesn't she look tired" thing is really more about, I think, a commentary on the government at the time - this was the point when the job was sending Blair really grey, he was making questionable decisions, and looked utterly knackered 24/7 compared to the smiling face he had been.
I think it's also worth noting she didn't just 'go against' The Doctor, she killed thousands of sentient beings as they were retreating. It's no small thing.
It would've been the same plot-line had it been a man. Harriet gets her moment of redemption later on, anyway.
RTD speaks a bit in the writers tale about how he writes women. He says he likes writing powerful women because it reminds him of his mother - in that household growing up his mom definitely wore the trousers how he describes it. His dad would bring home the money, but his mother was in charge and was a big figure in the tight-knit Welsh community he lived in.
The 'stripping away' thing seems strange but I think it's not really anything sinister - it's a byproduct of the fact that this show is about The Doctor who is (and always will be?) a man. RTD couldn't leave Rose or Donna with all that power and had to give a way to remove it, it's too much of a take-away from The Doctor otherwise.
Amy kept her being 'special' but it only actually does anythign in significant circumstances, whereas the 'powers' Rose and Donna got were stronger and more permanent.
I think to take away that RTD dislikes strong female characters is crazy purely because as much as you strip away any sci-fi/fantasy powers they might've gained to keep the stauts quo you can't ever really take away the fact that Martha was far stronger than The Doctor over the years The Master was in power, Donna was more even-handed than him and held him back, Rose was his rock, Joan was strong enough to let go etc etc. These are, arguably, bigger and more human showings of strength than most of what The Doctor does.
Even a villain like Miss Hartigan in The Next Doctor shows a really strong female character from him - so mentally strong that her mind survives being converted and takes control of the Cybermen. Say what you will about the quality of the show, but Gwen from Torchwood was a pretty good example of that early on, too. She's become more of a caricature in Miracle Day, but she was a great female heroine for the first 3 seasons.
