Referee did not fully understand accepted paper
As is the custom on this site (or at least it should be) let's assume the premises of the question are correct - that is that it is indeed a prestigious journal.

Do nothing. 

In fact no: celebrate acceptance in the way you find most appropriate.

The fact that some people misunderstand what you're trying to say is not a basis to act after acceptance. It might indicate that you presented your results in a not so clear manner — which would speak in favor of refining your writing for future articles — but that would not be an exception in the scientific literature. At any rate, edits (other than very minor ones such as typos) after final acceptance are generally not allowed.

If you see errors in your article that are not trivial and you feel need addressing, the appropriate way to handle this is to publish an erratum. I imagine most journals have a standard procedure for that.