Watching the climatic confrontation between the Doctor and Harriet Jones made me think of antanielle93's analysis of the four Hogwarts Houses as personality types. The Doctor is a classic Gryffindor. A hero, basking in thanks and compliments, doling out justice, death, and changes of government according to his own code. Prime Minister Jones isn't. The first encounter with her made her look like a Hufflepuff: "There's a lot of work to be done here, I'd best be started." But they're not the type to wipe out an enemy tribe after they've already surrendered (enslave, maybe--let all those strong hands go to waste?). The determination to protect "us" against "them" casts her as a Slytherin. I'm not sure I'd call her a pure Syltherin. More likely one of the Slytherin-Ravenclaw mixes, the Slytherclaws.* In a situation like this I'd describe the differences like this:
Slytherin: Kill them from hate/fear/disgust
Slytherclaw: Kill them as the logical choice
Ravenclaw: Produce an analysis showing they should be killed, but leave the dirty work for someone else
So PM Jones worked down the logic tree and ordered Torchwood to fire. We don't know what the crew of that ship was. All we saw was warriors. But it traveled all the way from Mars at sublight speed, so it's a reasonable guess that those guys don't have FTL. So the odds are there were families on board, the whole tribe migrating as a unit. Which she most likely guessed herself. But their innocent children don't weigh as much in the calculations as our innocent children. So the story ended with the danger eliminated and Earth more hidden.
But the Doctor liked the previous ending better. Lone hero standing up to massive force, winning honorably against treachery, sending forth the loser to spread tales of his prowess and add to his honor and glory . . . that's a great ending for a Gryffindor's story. Making his courage and skill a mere stalling for time until the machines settle the issue is a horrible ending. So he pulled out a memetic technology as advanced as the TARDIS and toppled PM Jones for ruining his story. Because he's the Hero and he's therefore right.
Great fiction. I'll stick with democracy in real life. That doesn't make PM Jones' decision automatically right. It's just an observation that relying on one Hero's decisions has worked out badly much more often.
So was she right? Tough call. I don't think the reasons she gave were sufficient to justify. I'd add one other. The Sycorax weren't going to go home and take up farming. They were just going to keep going until they found a rich world that wasn't "Defended", as the Doctor put it, and enslave those poor innocents. I'd've ordered Torchwood to fire.
There's another reason to be unsympathetic to the Doctor. The whole thing was his fault. I've read enough time travel stories to deduce the fundamental principle of time travel: The Conservation of Probability. In equation form:
If some highly improbable (P1) event with a good effect (E1) happens an equally improbable event (P2) with a bad effect (E2) must also occur to maintain the balance of the universe. They don't have to precisely match as long as the signs are opposite and the total comes to zero. The Sycorax would cause lots of damage compared to the benefits the Doctor would provide by hanging around London, but he's also much more improbable, so it balances out. In fairness to the Doctor, all those times the TARDIS gets yanked off to some unexpected time and place is probably him being used to balance out some improbable bit of evil.
Note that this works in different dimensions than good/evil. If slobby time lord the Bachelor visited New York leaving a trail of pizza crusts and candy wrappers, an alien robot with a tropism for styrofoam would arrive and consume an equal and opposite volume of trash.
Potential time travelers in my audience should beware. If you travel back in time and provide a huge knowledge boost in electronics and cybernetics someone else will come along and trash the school system so potential scientists will be reduced to illiterate drones. Oops, too late. Try not to do it again. The path of maximum probability has us making good progress and the best way to improve is to have the high-probable people already here work on it.
*Yes, that's where I put myself. All fan commentary is about projecting yourself onto the story. Move along.