If you find yourself in situation you really need it at any cost, then there is a chance it might be possible, because e.g. OneNote colors seem to be always from space (red 0~255, green 0~255, blue 0~255) so not only those limited ones. I expect pens to be flexible in similar way, too.
Basic high-level steps for solution are simple (also see
static void UpdatePageContent() sample at MSDN:
Programmatically export XML for OneNote page you need to change.
Modify colors directly in XML code of the page.
Programmatically import your XML back to OneNote page definition.
For more details on programmatic access to OneNote, search for
OneNote API. For instance, this is a valuable source.