If you’re using Safari you could drag the selection to DEVONthink’s icon in the dock. That creates a clean webarchive. When you’re done with clipping select all webarchives and use Data > Convert > to paginated PDF.
You might want to take a look at this Smart Rule script if you want to create the webarchives in a group structure. But it’s just a workaroud, see below.
@cgrunenberg would it be possible to add a preference that toggles the resulting record type when dragging from Safari into a window? Currently it creates RTF(D), would be awesome if we had the choice to change that to webarchive which gives the best results over here.