Well, historically the city guard would likely still be executed after the surrender.
But I see what you mean and... indeed. Which makes the screenwriters choice for the precise timing of even more baffling and clearly for shock purposes. It's deliberately forced so no one in the audience is supposed to sympathize with her after that. There's no moral shade of grey. At no moment your convictions are challenged. To people who claimed the White Wakers and the NK weren't interesting because it was manichaeistic... well, there we have it.
Honestly, Attack of the Clones, the second Star Wars prequel, with all of its flaws, actually manages to first showcase Anakin's issues, motivations and inner conflicts better than anything done with Daenerys in the last two or three seasons (which was basically looking depressed and snapping at Tyrion everytime he comes up with his idiotic ideas). Revenge of the Sith, then, it's Shakespeare next to this.
And saying the season having only 6 episodes isn't enough to develop the madness of her is also bad point, this gives over 7h of show. A movie have to do all that in under 1h30 and several do it greatly.
duduspace11 "Well, since we are estimating costs, Pokemon Red/Blue did cost Nintendo about $50m to make back in 1996"
Mr Puggsly: "Hehe, I said good profit. You said big profit. Frankly, not losing money is what I meant by good. Don't get hung up on semantics"