I started a similar project before Christmas. It has a whitelist feature, where you can list styles added using JavaScript. It may not be the perfect approach, but it's at least one way of getting around the problem.
It also supports lists of HTML and CSS files to search through. It can perform login, find duplicates, list used rules as well as unused rules, as well as count how many times each rule is matched in the markup.
Requires Node, can be installed with npm.