Well according to the Sims team in their own words and this goes still as recent as when I beta Tested Showtime for them - NEVER DELETE SIMS. Kill them, and let them die, move them on - do not delete them.
You have to understand there is a difference between deleting Sims we make in game and those made by EA and by the game generator - you will get the least problems using the method you mentioned with Sims downloaded to the game - but the sims EA has in the game are in the main game and will always exist - they are considered hardwired. Any sims that are in the game when you start a brand new game are these hardwired in Sims. They are programmed to continue to exist in the game actively until they die - then they are programmed to be a ghost unto they are moved on to the Netherworld. There is similar programming for the game generated service sims as they are placed in a pool in the programming of the base game and have to be treated as EA sims - they must die and must be moved on by the game or player in the way the game was designed to move them on. The game will keep giving these sims instructions and if they are not there it is going to generate some problems because they were not ticked out of existence in a way the game is programmed to do this. It will be the same situation for sims ported into worlds, so keep that in mind in user created worlds that come with sims without a save file.
I have heard though that sims cloned by the game as neighbor and sims you have added to the game yourself can be safely deleted as you mentioned.
Also from checking around I know that Pes awesomemod and Twallans mod can both be used successfully to eradicate the sims as both apparently tell the game they have died and gone to the Netherworld - of course it isn't that simple really but it is more or less what they supposedly do. I have not tried either to confirm there is no after affect or not, but with modders of that rank I am sure they know what they are doing and if they couldn't do it - than no one outside the game devs could. But yeah, deleting them is a problem - especially the longer you play the world the more problem it is going to create.
If you click on a ghost enough times you should eventually get the option for them to go to the Netherworld - which will move them on - i am just not familiar if this will work on ghost sims not on your lot you are playing. You also might be slowing down the negative affects with deleting sims by playing with SP off and no aging as the game will be less inclined to give the ghost sims constant commands - so you may be okay - but I suggest never to tell people to do that who play with any SP on and aging on, or their game is going to implode when it otherwise would not.
