Try changing windows' default color and test if it also changes the OneNote's color.
>but very few word processing programs seem to have a feature to facilitate that.
Almost every word processing program I've ever used had this feature. However, they're normal word processing programs rather than one-shot style software. I suppose you use it for the "reminder" purpose (it shows up a message once you boot your OS), right? Because if you're needing something which saves text files (a normal word processing soft), then even word can be changed in with windows default colors.
Pic related, Word and PDF in my win partition. I changed the whole layout colour palette to be some kind of dark-blue, but I haven't tested if the light blue from Word can be changed. I suppose you can, google how to.