Yeah, Ive tried deactivating the reactors and every order imaginable. Kill the boss, fight Kira, then escape the ship and still get the dialog for the start of the mission which resets the mission.
And yes to respond to the other guy, it does hurt your lvling progress. Im lvl 40 atm, and am hurting for quests as half of them I cant pick up because they are chained to your class quests (yes they still show a available quest marker, you just wont be able to grab the quest). Not to mention your stuck with just the 3 companions up to that point since Doc and the other one are tied to your class quests beyond that point.
I don't want to reroll though, its nice being the only Sentinal on the server No one seems to like playing Sent haha, (though I can see why its a pain in the *** sometimes but with gear Im know the class just *****)