I think the idea of retouching scans to the point of having a pure white background with sharp colors is a fallacy. Although I admire the efforts, I don't think it should be done. In fact, I've recently come across an interview (with Marie Severin) which suggests that the original comics (and I'm not just talking about EC comics) were indeed colored to take into account the ground color (the color of the physical paper medium on which they were printed). It's clearly stated that certain yellows, blues and greens were preferred over others, and that this was done for proper presentation with regard to the ground color.
For archival purposes I'd think it better to focus on getting a good scan, in a good resolution, and then "cleaning up" that scan sparingly... it makes no sense to do otherwise and is IMO a misrepresentation of the original finished work.