She doesn't think she has a choice at this point. The situation backed her into a corner. And as you can see from the immediate enemies she suddenly has (Varys) she was right to try to get Jon to keep his lineage a secret.
But she does have a choice. Jon has the true claim to the throne. He is the rightful Targaryen heir. If the good guys win, it makes the most sense. Given that she has his ear, she would likely be the power behind the throne anyway, but he is the rightful king.
Unlikely theory 3:
Jon and Daeny build a large wooden lion and leave it as a gift outside the gates to King's Landing and pretend to bugger off...
ETA: It appeared that the walls were overlooked by taller hills. Roll some big round boulders up to the top of those hills and let gravity do the rest.
Or have Drogon drop a cylindrical boulder and let it bounce up against the wall while stirring music is playing.
Unlikely theory: Dany, Jon, Cersei and all their advisors will get together, and decide that a monarchy is wrong, so they will let the people decide. They will have a constitutional convention and establish a representative republic with separate but equal branches--the legislative, the executive and the judicial....
In Daenery's mind, she did the moral thing Cersei didn't do--she fought besides the north to save them. Yet Cersei is probably seen as a savior and Daenerys has to be super careful not to scratch anything while they killed her allies and dragons and best friend.
I look at this as Dany being more qualified than Cersei to rule the totality of the Seven Kingdoms. Dany is better than Cersei, but still not the right choice.
I believe that is literally the entire point of her story arc. Will she blink or not in burning innocents?
I believe she will.
Ok, so let's say Dany spares the innocents. She doesn't use her greatest weapon--her last dragon. Clearly Cersei can't be allowed to remain on the throne, and how does she deal with the human shields?
I don't know if I call this a no win scenario, but it's something that the writers have to deal with and I look forward to that.
While we can argue that, the simple fact is that the Masters ordered the mass crucifixitioon of children as a way to intimidate people freeing slaves.
Do we know for a fact that all 163 masters did that, and did they all participate?
In the context that killing a Nazi is the same as killing a Nazi's victim.
Or killing a plantation owner is the same as killing a slave.
Except this plantation owner just murdered a baby.
Even the Nazis got a fair trial. And was every member of the German army executed? Every officer? Or only the top of the top?
On this show, sons inherit the title and estate of their fathers. Let's get creative. What if a father killed a child slave and was worthy of Dany's wrath, but had a heart attack and died the next day. Is it right to kill the son, who had nothing to do with it? How many other situations can we come up with where death is not justified?
Get creative--I'm sure you can think of plausible ones.
Let's also not forget, Dany's dragons murdered a baby. Yes, she felt bad, and yes, she locked up her dragons, but did she ever really atone for that? It was her responsibility, and she had a warning when they killed sheep.
Didn't it occur to her that a human could also be a victim?