Black turns into dark green after mode change.

[Ofnuts]

You can try to coerce the image colors into a colormap that is very close to the one Gimp would compute, but with a pure black entry. Starting with your RGB image:

• Image>Mode>Indexed (let Gimp create a colormap)
  
• Windows>Dockable dialogs>Palettes
  
• Right click, and "Import palette"
  
• "Import palette from image", and give it a name
  
• Edit the palette, set the darkest color to 0,0,0
  
• Back to Image, and Undo Mode indexed
  
• Image>Mode>Indexed again and give your palette
  

To edit the palette, three ways:

• Use Gimp's palette editor when you are in the Palettes list. But you lay have a hard time spotting the darkest colors
  
• Just edit the palette file (in the palettes subdirectory of your Gimp profile). This is a plain ASCII file. The darkedt color should be easier to spot. Once done, in the palette list: click the "<" icon on top right, then "Palettes menu>Refresh palettes"
  
• Mix of the two: use the Gimp palette editor, but open the palette in a text editor to locale the darkest color.