I'll start with an example.
Player X is really, REALLY good. He is playing on a small server. When a new map starts he alone kills 10 people from the enemy team, clearly causing his team to win. When the next round starts, player X's team is badly outnumbered to keep up the balance. However, player X has now gone afk, and doesn't spawn at all. His team cannot win without this mighty warrior against the enemy team's incredible numbers.
Same happens on the next round, and the round after that, and the round after that untill the map changes.
Now this kinda sucks, since the auto-balance is "blind" for this. So how about automaticly forcing the players to join spectators the moment the spawn time is over, if they didn't spawn that round at all.