I don't quite understand what you're saying.
Are you telling us that you originally had your photos in a separate folder, and decided to import all your photos into iPhoto? Did you have the "Copy File to iPhoto Library" button checked? If you did, then you'll have 2 copies of all those photos on your HD: one copy is in your original folder, while the other is in the iPhoto Library folder.
When you delete a photo from iPhoto, you're only going to delete the copy of the photo that's in the iPHoto Library. The photos you have in your original folders have nothing to do with iPhoto, and so iPhoto won't touch them. iPHoto will delete the photos stored in it's library. I say just delete your original folders since you don't really need them. Your photos just take up twice the amount of HD space as before.
HOWEVER...
If you check your preferences, and the "Copy Files to iPhoto Library" button isn't checked, then do NOT delete your original folder of photos.
If this is the case, then the reason the photos from your folder aren't being deleted is because they're still in iPhoto's "Trash" bin. When you delete a photo in iPhoto, it ends up in the trash bin on the left panel within iPhoto. See it? Good.
You need to "right click" on the trash bin and and click "Empty Trash" or something similar. If you do this, it'll delete the file from the folder.