One of the things that is awesome about "The Deserter" is how dubious it is. You can interpret Rex and Cut's conversations either way and not really be wrong. Umbara still hasn't fully cleared that up since the big scene at the entire last 3rd of "Carnage of Krell" both shows how far broken Rex is from his personal code and how incredible free thinking he is. I think the guy still has Fives beat at this and its only Cut who beats him out. Yet, Rex is still shown to potentially be unable to escape his programming when trying to execute Krell. Now maybe Rex was just overcome with emotion. We'll get there. I for one think what Rex said was sincere when he said the line Q has in quotes. Rex may not have realized it then. He clearly has a self imposed honor code that isn't some military code of conduct and Rex had gotten more flexible with it over time. Its interesting Rex also says something to the effect of, "I'm part of the most pivotal moment in the history of the republic. If we fail our children and our childrens, children may be forced to live under an evil I can't well imagine." in the same screen. Rex has already seen some of what he dreads in the Slave arc. Its to bad it wasn't elaborated on.