Filtering proxies don't know Javascript or Flash. I also don't want to worry about the parsing and semantic differences between the proxy and the browser: a lot of differences might arrise.

Putting ad-blocking inside the browser seems the most logical part, especially since you get the DOM already made so you know you look at the same data.

Javascript can always be used to smuggle unwanted content into the DOM. And there are far too many badly-written sites out there for most users to be willing to block Javascript entirely.

The only browser as minimalist as you seem to want is this one http://www.uzbl.org/

In all other browsers, they are basically a web OS. Stripping adverts out of web pages is well within a browser's remit. In particular, deciding what not to download is within their remit.