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
- 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.