If they ran off and rejoined, that would be cowardice in the situation. Sounds like these guys had to be tracked down and captured. They deserted.
Doubt the Rebellion would kill for that though. They likely wouldn't even track them down (no resources for that). Strip them from rank and dismiss them from service. They're not likely to defect to the Empire.
Death sentance would be more likely for someone like a traitor to the effort. Someone that allied with the Empire to help defeat the rebels.