The problem comes when I know one revision is older/smaller/incomplete in some way - the file checking that Hazel does is then a problem because they ARE different. This makes Hazel duplicate the existing file by append "-1" to the name of the file.

I understand this and acknowledge this is what happens because they are fundamentally different, however what I want to achieve is that the newer version is kept and the older version is trashed.
Say I have two files "Home.pdf" and "Home-1.pdf" I want to keep the second revision "Home-1.pdf" and trash "Home.pdf".
Following this I'd like to rename the file to delete the "-1" from the end of the name.
How would I go about doing this?