She took out Viserys (ok, it was Drogo that did that, but she could have intervened and Drogo would have listened to her. She had gained his respect by that point - which was the whole reason why Viserys got killed in the first place).
When Viserys wielded a weapon in Vaas Dothrak he was a dead man by their law. There was nothing that Dany or anyone else could have done. It is why Drogo killed him with molten Gold, You cannot carry a weapon in the city, and to do it is punishable by death no exceptions.
All you are stating is Dany surviving against people who were trying to take her dragons or eliminate her.
If anyone who kills their enemies is capable of going Mad and burning entire cities you can extend this logic to a lot of characters, but saying Dany "took out" Viserys by having him wed Khal Drogo against her will is a real head scratcher. Viserys took himself out, or Ilyrio did it by Counciling him to sell his sister to a Dothraki horse lord.
I thought the show did a poor job of executing this Dany into a villain twist. I'm fine with her burning King's Landing, but there are ways it could have been done to make sense. As it is, they just did not sell me on it. There is foreshadowing of all characters being both good and bad, and I can see Dany doing it, just not in these circumstances.