i think you may be right. this idea is probably more trouble than it is worth. however, as much as i personally dislike most uses of color in top-level and reply nodes (it doesn't really bother me on home nodes), i don't think that getting rid of all color is desirable yet (or necessary, as you've observed).
one thing that quite possibly should be fixed is the Saints in Our Book page. that page is largely unreadable with the dark theme, since both the text color and the background are gray (thank goodness for visual highlighting of selections (too bad it isn't XOR'd so that i could see my selection on a yellow page)).