I don't know how you do things, but I import my original photos from a folder in the Finder. iPhoto copies it to iPhoto/Originals/ then delete my originals because iPhoto copies my original photos to iPhoto/Originals/.
Why is that doing something in the finder causes dire consequences for iPhoto? If that was the case, shouldn't they have hidden the iPhoto folder? Does moving iTunes files around have dire consequences too? Picasa doesn't seem to have this problem.