IMO, if they are not in their seat at the table when the last card is dealt, the rules say they cannot play the hand. There is no consideration given to the blind putting them all-in. I think their hand should be mucked immediately at the end of the deal.
One additional note: if a player has left the table with only one big blind left in their stack, do we really expect them to return to the game?
We use a slight variation of this in our game. Because we have a rule preventing smoking at the table we don't allow players close enough to the table to try to play their cards. They end up taking a big puff and blowing it out while they lean over to check their cards. Not to mention that standing behind the table puts them in a very unfair position of being able to see other players' cards, then return to the table to play the hand.
As a result of this, we implemented what I call the "AIS" rule. If your Ass isn't In the Seat when the last card is dealt, your cards are deal, no exceptions. Players know this rule. So, if they leave their BB unprotected by being away from the table it's their fault they lose their blind, not mine.