At the point when the Doctor intervenes they are a threat to nobody, the only threat is from the Daleks. And there’s no suggestion in this episode that the Doctor opposed the Time Lords at any point in the war. He may not have been a soldier, but if he fought it was on their side, as far as we can see. The generals are not reacting as to someone who was frequently thwarted their plans, the Daleks are.
At the point when the Doctor intervenes they are a threat to nobody, the only threat is from the Daleks. And there’s no suggestion in this episode that the Doctor opposed the Time Lords at any point in the war. He may not have been a soldier, but if he fought it was on their side, as far as we can see. The generals are not reacting as to someone who was frequently thwarted their plans, the Daleks are.