this is as designed. If you pick a layer as input to the "Delete" tool. Then only the layer will be deleted. Layers are valid input to the tool. If the intent is to delete the data on disk, then specify the path to the data on disk, then both the feature class as well as the layer will get deleted.
解决办法
Right-click the feature class to be deleted from the Catalog window and select 'Delete' to delete the feature class permanently from the geodatabase.