Good question. From what I understand, it is true that everything is for our best. But we all have choices as well. If someone makes the choice to hit someone else, or negatively affect someone else, there are a few things happening: 1) A person is using free will to do something wrong. 2) G-d knows that it was going to happen. 3) It will cause a reaction.
Now, we are incapable of knowing why everything has to happen, and it isn’t our business to know. But if something happens that is beyond our control, that is seemingly bad, we should try to believe that it was for our best. But that doesn’t mean that such a thing had to happen in the way that it did.
It is possible that the outcome could have taken place even if the bad thing didn’t happen. Therefore, a person actively trying to do something negative shouldn’t require your thanks, because while it may be for our best, it could be that the effect of that action could have happened in a way that the person didn’t have to do something negative, and therefore, by him doing it, it may not have been the best way for it to happen. But I don’t know if it is WRONG to have hakaras hatov for that. Maybe it is a good thing to have hakaras hatov for it. I’m just trying to show the process behind it, which may help give a better understanding and enable you to come to your own conclusion.
Also, perhaps hakaras hatov is meant to be when you perceive something good. That is the definition, after all. And while something seemingly bad may be for our good, chances are we don’t see how it is for our good. At least not right away. And therefore, we can’t have hakaras hatov for it, until we can openly see how it is for our good.