If you do two short tables then the alternate plays. If that isn't an option then I guess the "alternate" should have responded sooner to lock up a seat.
We have a guy that hosts a single table deep stack tournament. 10 handed with up to 2 alternates gaurenteed seats.
I have played in as an alternate and won it. I hung out with everyone, got to watch how everyone was playing while not having to worry about playing myself which can be a huge advantage.