I know which post you're referring to. It's very hard to describe in a general sense what can be done and what shouldn't be done with persistent references. You certainly don't want to delete them. Or to be more accurate, you can delete them and then have TES4Edit Undelete and Disable References for you. It will put them in the proper state and get them out of your way.
The problem is that you never know what another mod is going to do. You might have another mod come along and try to reference the object you've deleted. If that happens, then the game will crash.
Here's a situation I ran into recently. In the Dark Brotherhood Chronicles, we wanted to modify some vanilla NPC's. Now I've been told it's safe to add dialogue and AI packages to them. If our mod is removed, the extra dialogue and AI packages will simply disappear. However in one case, the NPC wound up in the Tiber Septim hotel. This is what the game does if the NPC is placed in a cell that disappears when the mod is removed. Normally that wouldn't be a problem. The NPC will resume its normal schedule and return to where it's supposed to be. However in this case, the NPC had an AI package that made him stay in his current location. So our mod would require an uninstall script to move this NPC back to where he belongs before the mod is removed. We've taken steps to fix this issue.
So those are the points to consider. If you are modifying something that might be referenced by another mod, you can't just delete it in yours. In the particular case you are referring to, the modder simply replaced a door mesh with a different mesh - but the new mesh has a different name, which was required in this particular case. So it's not clear to me why he is running into the problem he's having, but I feel that moving the existing door out of the way and replacing it with a new door is the best way to proceed in this case.
Lastly, if your mod wants to do something drastic with an NPC, like killing him, then you need to clone the original NPC and use the clone in your mod. You will need to move the original NPC to an inaccessible cell. Once again, when your mod is removed, the NPC will be placed in the Tiber Septim Hotel and his normal AI packages should kick in so he returns to his normal schedule. If he doesn't have an AI package that will have him return, then you need to provide an uninstall script so that you can move him before your mod is removed.