Refuting a hypothesis in a dissertation
It is hard to give good advice on this without knowing the concrete dissertation and the expectations of your community. Hence, this is one of those famous questions where the right answer really is ask your advisor.

However, in the dark I am not sure why you would not just use Option 1 from your list - you had a (hopefully reasonable) hypothesis, you set up experiments and tested it, and found no evidence to support your hypothesis. Assuming that the hypothesis wasn't bad to begin with and the experiments were sound, why can't you just write it down like this?