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My advice would be to use the Select By Color option to select the color you want to make transparent. If it is a single indexed color, instead of various shades of it, you can set the threshold parameter to 0 - otherwise, experiment with the Threshold and select by controls until you mark all parts of the image you want transparent. After that,just perform Edit->Cut (don't forget to add an Alpha channel to your layer before doing that Layer->Transparency->Add Alpha Channel), and export your image as a GIF file. You won't need to convert to RGB and back to indexed mode if you just want to add alpha, and choose this method - it should work with the image in Indexed Mode.