When it is applied to a person, it is insulting. How bad the insult is depends on the context. It is never a compliment. It can be a mild or joking insult: "he's a heavy metal freak," meaning someone with an extreme, almost insane love of heavy metal music. It is not in itself a "bad word." It is not in your category #1. It can mean very improbable or very surprising, usually in the context of an accident or a death. "In a freak accident, a hunter was shot dead by his own dog."

Generally freak is considered derogatory when used to talk about a person. Not as bad as some of the insults that you listed but it should not generally be used to describe someone. That being said, the original meaning of freak was something or someone that was wildly out of the ordinary. Think, “freak show” from the last century where you could see a bearded woman or a person with three arms. Today, there are still many examples where it is used harmlessly or even where marginal groups have co-opted it. For example, a popular movie is called FreakyFriday. It’s a Halloween story where lots of strange and out of the ordinary things happen. You can also describe a situation as freaky - when a rocking chair rocks by itself, that could be called freaky. Or there are freak accidents - an accident that you would have never expected or planned for. Finally, there are some groups that want to celebrate being strange or out of the ordinary. Let your freak flag fly is a day to say I am going to celebrate and wave a flag about how I don’t fit into the normal confines of society.