One of the things I appreciated the heck out of "Gavial, the Great Chief", "Babel", "Lone Trail" and "To the Grinning Valley" is that we get a clearer image of the Doctor outside of the Main Theme. And what we've seen canonically is a someone who is kind and genuine to his Operators, but only really ruthless in battle to his enemies (from Ascalon). His desire to help people solve their problems (from Ray) is something that's always been present pre-Amnesia. Would he look at them like pawns? In so far as he knows that putting them in this mission is the best place for their abilities, like putting a pawn where it would be queen promoted. But what was also made clear in "To the Grinning Valley", is that Doctor is utterly, profoundly lonely. Even in the company of people, even when he's happy they won the day, he feels alien to them. Doc has friends and people interested in him romantically, but aside from keeping a distance so fans can fantasize, he keeps a distance because he can't bridge the gap his loneliness creates for him. And if you feel that kind of distance with people, you could possibly start treating them as just chess pieces. It's also worth nothing that war and battle can put you into a lot of situations where you need to sacrifice one important thing for another. Even if you're a master tactician some things will be lost and some of Doc's decisions would only appear ruthless but is in truth, necessity. Does that make Doc guilty? Possibly. If you recall in Lone Trail, Doc promises to Friston that he'll do things "just as he's always been." There's a tragic component to this from reading Babel; he could just go back to that despairing scientist who kills a kind, good woman. Or he could go back to that clever, heroic man who created a whole new plane of existence just to save his people from destruction.