The whole traitor thing... I thought it was pretty obvious who the "traitor" actually was from approaching the idea from the perspective of who the traitor could be, then eliminate anyone that couldn't be the traitor by paying attention to the course the game took. I only came up with one possibility. MB. Thinking about it for a second, MB had the motives and the ability to kill the Marines. MB wanted to invade the Federation but Madeline sabotaged the facility and sent out the distress call that Adam, the Marines and Samus received. Due to "interference" the coms of the Marines wouldn't work, something that MB would be able to foresee and protect against as she was on a Science Vessel of the Federation. But Samus Aran's Power Suit... she could not foresee her arrival and so could not prep against the bounty hunter's technology which is why for the most part, the Marines have issues where Samus has a relative cake walk when Adam authorizes the use of her systems.
MB played the "I'm Madeline Bergman" card when Samus corners her to cause Samus to trust her. She then goes on to "spill the beans" and gives a very believable lie by interspersing truth and "revealing everything." Since MB recognized and knew that Samus was responsible for killing the Metroids and Mother Brain, MB knew that Samus would attempt to kill resurrected Metroids and destroy the reincarnation of the rogue AI Mother Brain in order to keep the universe safe. MB then attempted to set Samus on the path of killing the genetically engineered Metroids (in Sector 0) that couldn't be frozen, an act that almost certainly would lead to Samus' death because she wouldn't attempt to avoid the Metroids, but kill them. Even if Samus figured out something to do in Sector 0 to survive, she would be out of commission for a while at the least and would be removed as the biggest threat on the Bottle Ship to MB's plans.
I can understand some people saying, "But what about that big machine that was driven by a Marine that tried to kill MB? That's a hole in your logic." To this, my response is that everyone assumes it is a Marine because of the power suit. But these power suits are full suits, covering someone from head to toe. In the Metroid world of the future, you also can be safe assuming that these suits are full of computers and electronics. In order to be worth wearing, they have to give benefits and throughout the game, it is shown that these suits allow the Marines to stay agile while still protecting them. This would suggest that the suits themselves have servos and other methods of propulsion to assist in movements so that they can be heavily armored enough to protect without restricting the movement of the Marines inside. Because of the electronics and internal systems, MB, using the fact that she is an android and telepath, could have controlled an empty power suit with a crude AI and caused it to attack her and Samus to discredit the idea that MB is killing off Marines in Samus's mind. In addition to this, the machine stays to fight with Samus, allowing MB to flee. The machine only comes out when Samus corners MB and after the fight, the "Marine" is no where to be found. There are also other portions of the game where Marines are alive then later dead where MB is.