You could try running each of your PDF files through the Create PDF task, in Workflow. You would set the Document option to None and tick the Optimize Resulting PDF option.
Note that this option attempts to optimize the PDF but may not necessarily succeed in doing so (in some cases, it may actually increase the size of the PDF!), but it’s something you can try.
One other option you can try: after you’ve sent each PDF to its intended destination, use a Create File task, which will replace the current work file (the PDF) with a new file that contains just a few bytes. This will ensure that even though temporary files still remain on disk until the end of the process, their size will be very small and should no longer be a concern. Note that using this option may have a slight impact on overall performance.
Let me know if that helps.