It hasn't always carried a negative connotation, and even today, it doesn't always carry a negative connotation. Here are some examples:
You'll find an archaic definition where freak is a whimsical quality or disposition. (ref #2)
Another archaic definition is to streak or fleck randomly. (ref)
A current definition, used in expressions like health freak means to be obsessed with something. So a health freak is obsessed with health (ref). An exercise freak (ref) is someone who is obsessed with exercise. Being obsessed is not necessarily a negative attribute.
I'll add this. Freak can also mean out of the ordinary (ref #2a and 2b). So a freak storm is a storm that is unexpected or out of the ordinary.