That article got me thinking about a few interesting things, particularly in line with Series 1 and the era of the Ninth Doctor (Eccleston).
The article talks about how the show uses the odd aesthetic trick, but generally the stories have more substance to them, and then it goes on to talk about contextual ethical choices.
The 2005 series had to work hard to be something substantial, that would resonate with the viewing audience. It didn't have the budget the show has now, nor quite the star-pulling power it has now either (though it still managed to pull in some truly spectacular guest stars, and Piper and Eccleston were 'fantastic')...
I now wonder whether it is coincidence that the first series of NuWho, which couldn't rely on those aesthetic tricks quite so much, is arguably the series that has the strongest ethical themes to date. The Ninth Doctor swims in ethics and is bookended by them - he was born out of a Doctor who had to sacrifice the Timelords to stop the Time War and his final story,
The Parting of the Ways, saw him preparing to slaughter the Earth to spare the universe from the Daleks, only for him to admit to being a coward "any day". In his series he had his closest friend Rose stand between a Dalek and the barrel of a gun in his control, he had the chance to "save the world but lose [Rose]" in
World War Three - a prospect he truly considered for a moment there. In
Boom Town he had Margaret's life in his hands and was initially responsible for whether she lived or died. In
The Unquiet Dead, it raised the ethical issue of the Gelth inhabiting the human dead...again, something that this Doctor was prepared to see happen.
I think the show tries its best to not stray too heavily into morals and ethics at risk of becoming preachy - it needs to remain just casual enough to entice the mainstream audience. We've seen The Doctor presented with a gun or the ability to kill on several occasions - whenever it's involved humans such as in
The Parting of the Ways,
The Doctor's Daughter or
The End of Time we've seen him admit he never would. He can hold the gun in his hands, but it would take a greater man to pull the trigger. Would the same rules apply to his own race? We've only seen briefly in
The End of Time such a prospect raised, and he had the opportunity to take alternative actions... but what if there was no alternate resolution and he had to either kill The Master or Rassilon? The thing is that in situations like that I think there will always be a get-out... the Doctor will always be given an escape from such an internal conflict, or an alternative will be presented...and that's that ethic ambiguity on display that keeps the show going
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As an additional side note, for anyone familiar with Buffy...or perhaps you don't need to be familiar in this case;
In Season 5, Buffy severely injures the main baddie of the series (Glory/Ben) and threatens her to go away and never return. Buffy then leaves to save her sister, and it then falls to Buffy's friend Giles who confronts this injured baddie...
BEN: "She could've killed me".
GILES: No she couldn't. Never. And sooner or later, Glory will re-emerge and make Buffy pay for that mercy. And the world with her. Buffy even knows that, and still she couldn't take a human life. She's a hero you see, she's not like us.
At which point Giles proceeds to suffocate Ben to death despite being a generally calm, peace-keeping character.
I think that reflects upon The Doctor very well too. The Doctor couldn't kill, and sooner or later he pays for that mercy as his enemies will always have one up on him. And as a lighter show than Buffy, The Doctor can't fall back on his friends to kill instead...insisting that he would never have asked Martha to kill in
Last of the Time Lords, and later the sense of shame and internal breaking he feels as his "Children of Time [are] transformed into murderers" in
Journey's End - an episode that later also saw The Doctor judge his Metacrisis form for destroying all of the Daleks. Later still in
The End of Time, Rassilon makes a point of the fact that The Doctor's last act in life will be murder as if it's a massive break in his character. And then in
The Day of the Doctor touched upon this as well with Clara pointing out that in her mind a man capable of violence and murder cannot possibly be The Doctor.
This raises one final question for me... I've made references almost exclusively to RTD-era episodes in this post, with the exception being
The Day of the Doctor which coincidentally borrowed a lot from the RTD-era. Now I wrote this post as I went along so no bias played its part along the way and I'm not inciting yet another RTD vs. Moffat thread, but rather am wondering whether the show did in fact explore more ongoing ethical points in its earlier reboot days when it couldn't fall back on the aesthetic tricks mentioned in the OP's blog post? Have more recent series given up that ethic challenge a little bit, as it might be something I've actually taken from thinking or over-thinking from this blog post