Ah, but that’s an old ham trick. The “lonely god / tortured soul” schtick is a very ham-fisted way of oversimplifying the Doctor as a generally nice person who is a hostage to fate and is haunted by his actions.
The original Cartmel plan conceived in the mid 80s was to go right back to the roots of Hartnell’s arrogant and ambiguous Doctor and expand on the question: who is the Doctor?
Why is he always getting caught up in conflicts if he’s (a) fundamentally opposed to war and violence and (b) could easily avoid those situations if he wanted to? Why do his own people think he’s unpredictable and dangerous, and not to be trusted? How can someone who’s not averse to abandoning loyal companions, but gives someone like the Master endless get-out-of-jail-free cards, be considered loyal to anything or anyone? Can someone as supremely intelligent and learned as him, really be a hostage to fate?
To some extent, the new series took all that right on board, but it’s still missed the point. The Doctor’s concept of morality, and ours, aren’t entirely the same. He’s always got the bigger picture in mind. Even when he feels conflicted, they are not the exact same conflicts a human would have.
Remembrance of the Daleks has some really interesting stuff on that level - McCoy was an utterly scheming and ruthless manipulator about to commit premeditated genocide, AND a concerned pacifist begging Davros not to commit mass murder - in the same scene.
And the sheer fact he was able to do it without doing the either the tortured guilt/angst routine or the “kind face/game face” cliche, was for me what made him the only Doctor so far to really get it.
The Doctor, in that story, point blank refuses to show either pity or mercy. By the end it’s apparent he not only engineered the entire Hand of Omega situation, he was actually waiting for decades for the Daleks to take the bait...
At the end, Ace is sufficiently conflicted to question whether they did the right thing, and the Doctor merely says “time will tell”.
That’s what made McCoy a genius - with him, you still think the Doctor’s a benign force rather than a “lonely god” or angry megalomaniac, even when you’ve just sat through ninety minutes of drama indicating that the Doctor’s mindset is more along the lines of, “I set someone up to explode a populated solar system, and it killed billions, but I’m not conflicted about it, at all, ‘cos I can see the big picture and you lot can’t.”