Inkscape really is not designed for this kind of task. It excels at vector drawings, but since you're both importing and exporting raster (i.e, pixel-based) images, an image editing tool such as GIMP would be more suited for this. The reason the image appears to lose "sharpness" is because...

I have (and will be creating) a number of diagrams which will be used on both light and dark backgrounds. I would like to be able to create a single drawing and parameterize the colors, so that I just change the definitions of "foreground", "background", and "accent" to...