What I did was make a folder in my Documents folder called "Printed PDF files for OmniFocus". I then made an alias to that folder, which I named "Send PDF to OmniFocus" and placed in ~/Library/PDF Services. I used Applications/Applescript/Folder Actions Setup to enable folder actions for the "Printed PDF files for OmniFocus" folder, and set it to run the AddFileToInbox_Droplet file when a file is put in that folder. This saves a copy of the file in a place where it won't be deleted if my system is rebooted.
Note that the script does not embed the file in the OmniFocus database, so if you are syncing with another Mac or an iPhone/iPod touch, you won't be able to view the file. It isn't clear to me if it is possible with the current Applescript dictionary to tell OmniFocus to embed a file. One possible workaround for this difficulty would be to arrange to store your files "printed" to OmniFocus in a common location, such as a MobileMe folder or a
Dropbox folder which would have the same name and be reachable from multiple machines, and then it wouldn't matter that you were only syncing the URL, not the actual file.