How do I change bond colors to something besides a different hue in Coot?
You could try other visual differences, like make what you're interested in ball-and-stick, and everything else wireframe, like in this example:

.

.... Because, from: http://www.ysbl.york.ac.uk/~lohkamp/coot/doc/coot-python.html


  procedure: hilight_binding_site (imol, centre_residue_spec,
  hilight_colour, radius): hilight-colour is specified in degrees (round
  the colour wheel - starting at yellow (e.g. 230 is purple))


It looks from this like you only get to choose Hue (color_map_rotation) and not Saturation or Lightness, even with the script interface.

However, text can be full RGB


  3.28.3 (set-font-colour red green blue)
  
  where:
  
  red is an inexact number green is an inexact number blue is an inexact
  number