Q: Can I permanently delete an app?

Yes

go to the apps section of your library select the app you want to delete. Hit the backspace button or right Mouse click and select delete. Select Move to trash, Empty Trash and it should be gone. Then when you sync your devices it should be removed from them.

It is already in icloud as a previous purchase so deleting it has no effect on icloud just on your local machine. Besides I am not sure but if purchases from itunes store are in the cloud they are there as only pointers to files on Apple servers. That is why you do not change the space used in the icloud

If you are concerned about storage space so apps need deleting from the cloud then this article may help

http://www.ilounge.com/index.php/articles/comments/deleting-app-data-from-icloud /

By any chance do you know if I can permently delete an app on an iPhone if I don't

Connect it to my laptop ... I need to delete something off my exs phone while he's still on my account, he's locked some photos in a secret password locked app call "my utility's" and he's threatening to put them on the Internet, and as you can tell they are personal, Please any suggestions would help

Jeweler wrote:

 

I do not use iCloud for any storage yet there is almost 2gb of the 5 used.  The only thing I can find in icloud are deleted apps.

The iTunes in the Cloud service does not use your iCloud storage. That is probably email.