Of course it mattered that Earl was alive and Johnny would figure out what happened when they were on the flight back to New York.
Eddie put the gun away. He heard the gunfire in the room, knew Johnny thought Earl was dead and that Eddie had some part in it, and didn't know what Johnny might do when he saw him. Eddie wasn't sure whether he would need to use the gun on Johnny but knew that he had better keep it on Johnny until Johnny saw Earl and Pauline. They were in this together but Johnny didn't know it yet. When he saw Earl and Pauline, he knew.
The sooner they got back to New York and sorted out who else wanted The Needle dead, the better. When they figured that out, they'd know who also wanted to take over. And they had to find out what happened to the others. Did they know that things didn't go down according to the plan at the El Morocco? The guys who showed up in Johnny's hotel room must have figured it out and they were in no mood to celebrate with Johnny. If they came after Johnny in Vegas, their cronies must have gone after the others in New York. Did the others have the same premonition that Johnny had? Were they as smart? Or were they already dead...the first victims of the new battle for New York?
They were on the first flight from Vegas to New York. As they boarded the plane, Johnny and Earl took two seats together with Eddie and Pauline right behind them.