And isn't this what everyone should really be doing anyway so that they own their own work and words?

As I've heard in the Indieweb chat: "Silos gonna silo."

Does the script Audrey Watters is using really stop people from annotating her site directly?

Based on my quick test, one can still (carefully) use Hypothes.is to highlight and annotate her site, but the script at least prevents Hypothes.is from showing that annotation. When visiting her site with Hypothes.is' Chrome browser extension on, it does show that there is one annotation on the page. It then requires some hunting to find this comment.

I’ve spent some time thinking about this type of blocking in the past and written about a potential solution. Kevin Marks had created a script to help prevent this type of abuse as well; his solution and some additional variants are freely available. — {cja}