The Doctor's attitude to the military dates back to his childhood, according to "Listen". In that episode, he sought shelter in a barn so that other child wouldn't see him crying because he had learned he would be going to the army. He didn't want to go the army. Why? Unfortunately, like a photograph, we have a snapshot of a moment and don't know the before and the after (the context in which the moment is a part of). We don't even know who the woman and man were. It's frustrating not to have these answers. Hopefully, someday they will be answered. (Or not.)
The Doctor has been waging conflict against other people and groups since the First Doctor. It's not "The Daleks" where the Doctor changed; it's the largely forgotten serial "The Sensorites". From the book About Time: The Unauthorized Guide to Doctor Who, Volume 1, page 73:
So it's worth noticing that it's the first time the Doctor, rather than Ian or Barbara, is the instigator of much of the action. In fact, it's the first time the Doctor saves a planet not simply to get his Ship back but because it's the right thing to do.
So let's reiterate: this is quite possibly the most important Doctor Who story of all. The key scene comes in episode four, and most people miss it. Ian is cured of his illness: the nature of the "plaque" has been discovered, and the Doctor has done everything the First Elder requested of him. And yet, the Doctor decides to go and investigate the water supply. He isn't doing it out of idle curiosity, and he's aware that it might be dangerous, but he elects to go into a hazardous place and save a planet because he's good. It's at this precise point that Doctor Who as we understand it comes into existence.
The Doctor has killed many lifeforms in his lifetime, either directly or indirectly. The agent of a person is the person himself - so, when a companion kills under the orders of the Doctor, the Doctor is killing. This is the concept of agency. And, this was before he became the War Doctor. I am still attempting to understand why the Doctor didn't became the president of Gallifrey during this crisis. He was considered the president of Gallifrey up to the time of the Seventh Doctor, and, as president, he would have more power than a single individual waging war against the Daleks.
The latest episode was playing coy with its references. There was a reference to Barbara Wright, who was a female teacher at Coal Hill, and the fish people of the city of Atlantis from "The Underwater Menace".