All colors are defined in ckeditor / ckeditor.js. This is a thumbnail file and therefore difficult to read. If you search in colorButton_colors, you will find the following definition:
colorButton_colors='000,800000,8B4513,2F4F4F,008080,000080,4B0082,696969,B22222,A52A2A,DAA520,006400,40E0D0,0000CD,800080,808080,F00,FF8C00,FFD700,008000,0FF,00F,EE82EE,A9A9A9,FFA07A,FFA500,FFFF00,00FF00,AFEEEE,ADD8E6,DDA0DD,D3D3D3,FFF0F5,FAEBD7,FFFFE0,F0FFF0,F0FFFF,F0F8FF,E6E6FA,FFF';
Just delete or add the desired colors.
Hope this helps!