Inserting PDF files via the Image icon in ckeditor. Is there a better way?
The canonical "Drupal way" is to keep files in file fields. You are free not to display them in your theme for readers and only keep links in body. Having them explicitly linked to a node has some advantages: you can keep track if files are used or should be deleted, you can display them in views, in search you can possibly add "with attachment" option and so on.

You can write a CKEditor plugin - copy image uploading one, change output from &lt;img src=" to &lt;a href=" and you have what you wanted. It's what you want, but be careful, you might regret it in the future if you'll ever need that node-file relation.