Fastest way of thurning this into a hightmap?

[Mazahaka]

This is compressed and saved as .GIF for file size, original can be found here:

[Plasma_Wolf]

It's virtually impossible to do this in a fast way with the supcom map editor. The map editor imports .raw files for heightmaps and textures. The .raw file has the pixels ranging from 0 to 255 in grayscale. The closer to 255, the higher the corresponding place in the eventual map.

With copying colours from your screenshot you can use photoshop to extract green and turn it into white for areas that you want to be green in the eventual map but you cannot use this for the heightmap. Then all the green bits would be high for example.