Due to Business requirement is it possible to set "Overwrite existing file?" unchecked by default when uploading document. This change would let users prompt when overwriting document, at the moment due to user error documents are overwritten.
I would recommend you to write a custom Feature which has AdditionalPageHead delegate control to un-check the "Overwrite existing file" (using jQuery) option while uploading the documents.
Note: Manually updating the Upload.aspx in 12/14 hive is NOT recommended!