Martin,
File uploads being on is not really a problem as long as you take precautions and code the upload functionality with checks. The same applies to many php functions.
If you're looking for automated ways for clients to "send" documents to server without upload functionality, I can think of only complex work-arounds. It would be much easier to take the time to understand the security considerations of file uploads and implement with care.
More advice than actual how-to unfortunately.
-m.