Same deal for me. The Kerbal bugs out, maybe because he is still attached to the ladder when the ship is destroyed. It seems the part by part destruction changed and always starts with the command pod. This also bugs out chapter 4, when reaching the oil platform, the mission immediately fails, due to the Kerbal dying in the command pod.
Edit:
Looks like, the parts are always destroyed in the order they were built. So if you placed the command pod first, it is destroyed first. This seems off and should the exact opposite. So this might be a bug in the current KSP version.