We are also not getting into the whole way the society works and is so hypocritical. Dany's enemies before coming to Westeros are mostly slave masters, so bad evil slave masters. Really though there isn't any functional difference between a slave master in Essos and a Lord in Westeros. A peasant in Westeros is essentially a slave to his Lord. The peasant doesn't own anything, not his land, not his crops. It's all the Lords. A peasant can't say no to the Lord. If the Lord says "hey i need more crops from you" The peasant cant gripe and then vote the Lord out. If some Lord shows up and says "hey leave your home we have a war to fight 1,000 miles from here." The peasant cannot refuse. She is tearing down this evil, awful system in Essos so that she can go place herself at the very top of basically the same system in Westeros.
Also the Dothraki owned slaves. The Dothraki would attack, destroy, rape and enslave entire societies of people. Dany doesn't punish them. Why not? She can use them. Why are the slave masters so bad that they deserve crucifixion while the Dothraki don't? Or the Lords of Westeros don't?
You have watched the story from the perspective of Dany being a protagonist. So to you the people she has gone against have all been bad. Its GoT though so no one is really all bad, no one all good (with a few exceptions). The 163 men she crucified didn't all deserve it. Maybe some did but even those were not crucified out of justice they were out of revenge and to use to spread fear of her. The Tarly's were not bad guys. The Khals she burned to death didn't deserve it. None of them had done anything worse than her "sun and stars" had also done.
The fact is Dany has often treated people with brutality and cruelty. She's done it over and over again. And if you are watching the show thinking "yay!!! go Dany kill those slavemasters! they are all so bad!!" The I think you are missing the show. I mean if we are all so concerned about innocent lives then our best characters are Tywin Lannister, Walder Frey and Roose Bolton whose benevolence in planning the Red Wedding lead to untold thousands of lives being spared from dying in the war.