Apparently you shouldn't delete things like spawn points, but isntead disable them or put them underground, is this true?
Just thought I'd chime in here... NEVER move a spawnpoint below the terrain. Spawns which are placed below the terrain, either due to misplaced markers or pathgrids often cause crashing, If you're editing a vanilla cell and moving around pathgrids or spawns, users of your mod should not visit these locations until after the world has been respawned for exactly this reason.
It's this which is a common cause for some people having CTDs from your mod while others with similar setups run it fine. If you're unsure if this is the cause, always test from a new game.
For vanilla objects, although disabling is a better option, deleting non-persistent objects shouldn't cause any serious problems. If however you're basing a .esp off content in another .esp, disabling is the only way to go, and
still requires deisolation to prevent crashing as one .esp tries to remove objects which don't exist within that .esp.