What other options do you see? Searching and manipulating DOM in JavaScript wouldn't be faster than a single CSS stylesheet. Remember that there are >20K rules in play.
If there would be an option for a extension to hook into DOM element creation (i.e. when browser parses HTML and builds a tree, it'd call some user-defined predicate function) - that would possibly solve the issue.
I believe CSS is slow because of cascading nature - it requires re-compiling it from the very plaintext source on every page view, to combine ad-blocking rules with others - this certainly could be optimized (if browser side would provide tools for that). No idea about horrendous memory usage, though.