Young tampered with and later hid the evidence of Rush's crimes. Later, he ordered away all witnesses so he could physically assault Rush, and leave him to die. After that, he returned to the Destiny and lied about the entire incident, claiming that Rush died in a rock slide.
The only thing Young has done is nearly validate Rush's insane reasoning. And when Rush returns, Young will immediately be caught in a lie (Rush's death). And the only way for Young to get out of the situation would be to admit to another lie (Covering up Rush's murder frame). And admitting to that lie will only reveal that the only 'justice' Young is interested in is his own, twisted sense of the word. Not unlike Rush, in the end.
The only way I see the writers getting out of this situation is the following: Rush returns to the ship, pretends Young's story about the rock slide is true (he'll say he miraculously survived), and holds the true story over Young in order to reassert his position on the ship without any consequences for his murder frame. Eli, of course, will go along with this, because he'll do whatever the writers want of him.