I believe that this snippet from the first answer may be helpful:
https://stackoverflow.com/questions/5370326/changing-all-the-colors-in-
lilypond
But from what understand, more useful may by this part of documentation
http://lilypond.org/doc/v2.19/Documentation/internals/contexts
or rather this
ht
I don't see any answer, so here are my two cents.
Here you can find snippet, that colors note heads depending on their
pitch and name:
http://lilypond.org/doc/v2.12/input/lsr/lilypond-snippets/Pitches#Color
ing-notes-depending-on-their-pitch
All you need to do is modify the list associating pitches