How did the notion and punishment of desertion fit into feudal armies, given that it plagues both Robb and Tywin?

Well, it was a bit more complicated because feudal armies only served for a limited period of time, so if your war went over the allotted time, people could legally leave. Holding them in place meant supplying and paying them, offering them plunder and conquest, etc. 

Now it wasn’t that your army would disappear completely, but it was a lot more normal for armies to wax and wane with the season, and why there was a campaign season.