Well first of all, can switch sky boxes in game by selecting and deselecting the "Show Colored Skyboxes" tab in the options until you get one you want. But if you really want to totally remove it...

It is the Star a solar system is in that determines what skyboxes are available. So go to the mod's GameInfo folder, find say StarBlue.entity or whatever, and open it in notepad (I believe you don't have to worry about converting with SoGE). I'm afraid I don't have the file in front of me to tell you the exact line, but there is a section that is a list of every skybox that can appear at that star. Take out the ones you don't like and reduce the count at the start of that section, and repeat for every star and that should work.

I know, I've played the mod. The reason it's on every star is because they told it to be on every star, it doesn't change that you still have to remove it (actually I think they have more than 1 skybox that looks like that) from every star.