The exact same thing happened to me. Was hurtling along the ground in a plane, out of control, then went EVA as a last-ditch attempt to save Bill from a fiery death. He hit the ground, ragdolled for a while then bam, Kerbin disappears. Restarting KSP seemed to fix the bug, but the damage was done. Bill was missing in action and the debris of his plane was on an escape trajectory. Weird.