Players retiring is not by ATP choice, but by player choice. The players basically announce they won't be playing any more tournaments, which does not concern the ATP. ATP doesn't have to do anything. Players can change their mind and continue playing despite announcing not playing anymore. They shouldn't be taken out of the rankings unless the player asks this or the player has violated parts of the conduct code. It's correct the way it is now. Retiring is not like signing a contract with ATP. In fact, the player doesn't even have to tell the ATP he is retiring (maybe except for commitment players).
I know it's by player choice of course, but it's the ATP's computer, other sports when players retire remove said player from their stats etc. so why not tennis, and you can't expect the ATP to wonder if that player will come back, which they usually probably won't, they can't be dealing with that, as I said before it's not fair to active players to have retired guys taking up their spots, like for instance when Roddick made a big deal of his retirement, I think it's quite certain he won't be coming back, so there is no point in having him still in the ranking.
When is a retired player removed from the computer btw, when the season ends?