Research on color preferences (I don't remember seeing things specifically for head-aches) tend to be mixed (see MacEachren's How Maps Work for an overview). I personally do not like when there are multiple, fully saturated colors (and that example gives me a headache as well), but user studies typically do not find unanimous preferences, e.g. some people like red as opposed to blue, some people like saturated instead of pastel etc. (I'm making the jump from preferences to head-aches, so let me know if there are actual studies about head-aches and if they have different findings.)
So in your situation I would likely change the areas you are digitizing to lighter pastel shades (and/or make them semi-transparent), and then change the purple background color to either a lighter shade or change it to a different shade of grey. I'm skeptical if there is advice that extends to everyone though.
You could also try inverting the color scheme, using a dark background and then having the features light (see here and here for some examples on my blog where I discuss this). The UX site has several discussions of this, and some of the recommendations also talk about the background ambient light. You may consider trying to invert the color scheme and if you have the ability to dim the lights in your office. Below are some references from the UX site on the topic of dark backgrounds in which it comes up in the discussion:
(Some of these are marked as duplicates of the others, but they did not merge the answers so there are very good answers to each of the questions.)
