User blog comment:SpookyBoogie27/Light Novel Spoilers/@comment-8.28.150.75-20140208183202/@comment-24501441-20140208202000

“—It was the God from the Bible. That God sure was amazing. He found 666 even before any of us and put thousands of seals on him. Maybe, that may have been the cause of death of the God from the Bible. After all, there were so much powerful seals that would be regarded as a forbidden level and it wouldn’t be weird for a God to die after using those kinds of seals. So it’s a plausible story for the God from the Bible to vanish if he took part in the war between the Three Great Powers due to fatigue.”

It is implied that he died due to being in a weakened state. That, along with the fact that all three factions knew he was dead, is another indication that he died as a casualty of the war, not just disappearing during the war. But I do admit, with the lack of details as to his death, you bring up a good point.