Indies, as a group, should not be so eager to leap into hostilities not aimed at them (especially since the academy is affiliated with them, which is where the main story is centered at, and building Commerce means giving Indies a foothold on your world). Rogue fleets like salvagers and mercs are fine.
It is a reason why I dislike their auto-hostile over so-called "atrocities" not aimed at them. Makes them look like they pick sides, namely with the enemy, and at that point, they become an extension of the enemy faction (even if they still wear the indie flag), and thus, a target to be destroyed with the enemy they side with.
I expect the Indies to not go hostile and stay calm and indifferent at the Diktat if they sat-bomb the player's fuel planet, but if the player returns the favor at Sindria, Indies will get mad. I would conclude the so-called Indies are Diktats wearing the Indie flag, and wearing the Indie flag will not save them from getting nuked back.