At the end of the episode we see Eli showing Young that Rush and Wray are plotting against him with Keno footage. Maybe the split wasn't as deep as you thought. Or maybe his confidence was restored when Rush came back alive.
I highly doubt it. Much of the episode involved Eli becoming less and less happy with Col. Young's orders. This culminated in Eli's big exclamation to Young during the big battle: "You should have thought about that before you decided to get rid of Dr. Rush." That was a critical moment in the episode and can't be overlooked. Young managed to make Eli even less happy when he ordered Eli to fire on the ship with Chloe still on onboard, even though Eli was telling him that it would risk blowing up the whole ship.
Yes, Eli was still helping Young spy on everyone during the final montage, but there was something in there that caught my eye. There was a moment where the camera was on Col. Young, and he made a quick glance away from the screen towards Eli. To me, it looked like a nervous or even suspicous glance. I don't think Col. Young is 100% trusting of Eli anymore. After all, Eli had actually stood up to him for the first time earlier. The main reason Col. Young has always depended on Eli is because he has always seen Eli as the only scientific mind on the ship that he could reliably control. The fact that Eli is seriously questioning him now will probably put a big dampener on that.
Eli has always been the character most caught between Dr. Rush and Col. Young. While he respected and obeyed Col Young, he has always been the person who respected Dr. Rush the most, and was the person on the ship closest to Dr. Rush. Now that the next episode is going to involve an actual power struggle, I bet we are in for an Eli-centric episode.