I think a lot of what is happening with Dany is now just retcon'ing and trying to make the square peg fit the round hole. Her destroying the scorpions, Iron Fleet, Golden Company, Kings Landing Guard...all perfectly fine. Inch-by-inch destroying Kings Landing and all of its innocent civilians flies in the face of her character for the entire series up to that point where she says fvck it and makes a move on the Red Keep. Her killing treasonists, masters, and dissenters has a place in this universe...the innocent...you're right, it doesn't make a ton of sense.
The end of Varys seems very silly and was a microcosm of the plot issues the writers face. Varys is a nuanced character driven by dialogue...you don't really get that by the end.