I like your decision mooredog and your warning to the player. I think that is fair.
If I see a player leaving the table with the player still having a live hand,, I would warn the player not to leave his seat and the dealer should as well.
In general, i believe the "at your seat" rules generally take precedent over the others. The player abandoned his hand. I wouldn't actually know if he intends to come back. So I would turn over the hands because of the all in situation, (to determine if any additional penalties are warranted) but award the pot immediately to the remaining player, and return any excess uncalled portion to the utg stack if utg had the caller covered. I can accept Chet's suggestion, but if you give such a "grace period" by waiting until the river is dealt to declare the hand dead, you are essentially saying that you can revive an already abandoned hand (the hand was abandoned when he left the table) which I personally think is problematic.