For me, one difference between Sansa/Arya and Dany is the Stark girls knew Ramsey and the Freys were guilty of atrocities against them/their family.
With Dany, the point has been made, even on the show, that for those children who were crucified, Dany didn't get those she knew were guilty. Some or all of them may have ordered it but it was never established exactly who did. If I'm not mistaken, she crucified the en-slavers as punishment for what was done to the children, not for simply being en-slavers.
Then there is the guy she fed to the dragons. Again, if I'm not mistaken she herself said she didn't know if the guy was guilty yet she executed him anyway.
Dany targeting civilians (instead of just going straight for the Red Keep) can't be explained away and I can see how she'd do something like this given I have seen her execute people who might be guilty. For me, it was a slippery slope.
Going back to Ramsey, for me, he dug his own ditch. He purposely starved his hounds so that he could feed Jon and whoever else to them.
If you set a trap for others, you will get caught in it yourself. If you roll a boulder down on others, it will crush you instead. Proverbs 26.27
Now, had Sansa starved the hounds after Winterfell was taken back then locked them up with Ramsey, I would have had a problem with that.