Napivo -- You can maybe sort of do this by recoloring a certain graphic file in the game's folders, depending on why you want to recolor it.
If what you ultimately want is to be able to pick out neutral planets from destroyed and unscouted planets, then you'll need to file a request on Mantis like Pumpkin suggested.
If your main concern is just making it faster to tell nonthreatening planets (of any type) from known hostile planets on the galaxy map, then the workaround below may suffice.
Go to: <wherever you put AI War>\Arcen\AI War Fleet Command\AIWarGame\RuntimeData\Images\GalaxyView
Find PlanetSmall.png
That's the graphic that gets used by planets that are unscouted, destroyed, or neutral (no one has a command station on it). You can open it in GIMP or whatever graphic editor you like, and recolor it, change the shape, etc. Just be sure when you save not to strip out transparency (the alpha channel) because the background is transparent -- a non-transparent background would look pretty ugly on the map.