STOP that thought right now!!! Photographs have been manipulated since day one....you think Ansel Adams didn't manipulate in the dark room? ALL photographers manipulate their photos. PLUS, that's the second artistic side of a photograph, you can change that one photograph a million ways, dark sky, heavy colour, light sky, just one colour, blown out features, etc. etc. etc.
Be proud of how you want your photograph to become.
BUT, i know how you feel...I felt the same way in the beginning until you realize that's the beauty of art.