"차라리 재준이가 완벽하게 사라졌다는 사실을 내가 받아들여야 하는 게 아닐까."
=> Isn't it like I should now accept the fact that Jaejun has disappeared beyond any doubt.
Ending forms like 아닐까, 아닌가, -던가 are bound to appear a lot in this kind of first person narratives, as they represent questions directed to oneself. If you're contemplating suicide as the protagonist of the story does, it's only natural to ask all these agonizing questions of what-ifs, whys, and hows. In fictions, it would be even more the case because mixing in questions and other forms makes the story more interesting and natural than constantly repeating monotonous plain forms.