Are you playing on an unmodified game? Mods can affect the storyline, but I don't think there are very many mods that alter the storyline on Malachor. More importantly, did you activate all four generators?
The link you posted refers only to changes that TG is making to Malachor. As I understand it, they are restoring a pile of stuff cut from the planet. Unless you are using the leaked 1.0b8 version of it, you don't have to worry about it.
- Star Admiral