I did some more research on the MarkForDelete command. It apparently flags that item as deleted from your savegame, so after a cleanup it is gone. Only option is to load up an old save from before the command was saved. I found a recent save, found the tree still in the worldspace, and was able to add it back to Whiterun, while still keeping it in the worldspace, so you can see the tree from outside the walls. Mission successful.