You can do it with just one layer. Open your png in gimp, then go to the

color select tool, set the mode to 'add to current selection', the Threshold to about 25 or so and then click on the orange parts. this will select any and all orange and if you click around enough, it will select every pixel with that color.
Once you have a satisfactory selection, go to the paint brush tool

and pick a suitable color from

the color swap. Click on the foreground color (default black) to get a color editor. Then paint on the selected areas that are the edge of the icon, don't paint on the middle red exclamation point.
Once done, export to png and you're golden.
Hope this helps.