I have a theory on how Murobashi Etsuto was killed. It's not that good, but here goes...
I'm suspecting the murderer is Andou Satoru. He and Murobashi were planning on doing something that required the conductor not to see them in action. Andou was in Murobashi's room when Noto and his bell caused the first disturbance. I'm not entirely sure why the bell was giving Noto problems to start, but I'm guessing Andou had set it up without telling Murobashi. Just as Andou and Murobashi had called a hidden cellphone in Idenami's room to cause their disturbance, they heard Noto complain with the conductor outside, so Murobashi poked his head out into the hallway to make sure their plan wasn't being disturbed. He told Andou, who was in his room, that everything was fine and that the conductor seemed to make a mistake. This is when Andou committed the murder. Andou had forced the disturbance with Noto and the conductor previously to distract Murobashi enough so he could pull out a silenced pistol. Because they were the only two in the room, it would be difficult for Andou to pull a pistol out of his jacket without Murobashi noticing and putting up a resistance. Now, Andou had the pistol out and was aiming it from behind his back. When Murobashi unexpectedly sat down to the left of Andou, Andou fired the gun. The blood stains on the wall of the room suggest the gun was at a relatively low height compared to Murobashi's head because the blood splattered at an upward angle, and if Andou was aiming from behind his back then that would be possible. As Murobashi was shot, he dropped the cellphone that called Idenami's room on the ground and accidentally disconnected the call. This was why the sound in Idenami's room seemed to stop just before the conductor got to her room. Hastily, to set up the distraction again, Andou called Idenami's room once more to start up the sound. Meanwhile, he placed the gun in Murobashi's right hand to make it seem like a suicide and, when he was sure the conductor was distracted with Idenami's complaints, exited the room with the cellphone in his pocket unnoticed and proceeded to set up the chain in a fashion Kyuu suggested to make it seem like a locked room murder. He quickly entered his room, hearing Conan and the gang approaching, re-exited his room just as the group reached Murobashi's room, and pretended to be concerned with Idenami's problem and that he was in his room the whole time.
That's my not-so-great theory. If anyone has anything to add, feel free. I know I have a lot of holes in my deduction, but it's the best I can do with what we have.