The solution I came up with for this problem was that I would use the PHP native FTP methods to log into my account via FTP and CHMOD the folder I wish to upload files to (changing permissions to 777), then upload the file using PHP (move_uploaded_file), then when the upload was complete, use the PHP FTP methods to CHMOD the folder back down to 755, or something more secure. This way I don't have to leave my folders globally writeable except when I was explicitly uploding. I know it is a bit of extra work, but it means I don't need to worry about leaving my directories exposed. This could also be used to set files as writeable and then you can set them back after you are finished.
I also experienced the pain of the "nobody" ownership on files. But ended up writing my own PHP script which would delete directories using (unlink) in case this ever happened. I can PM you this code if you would like, it came in handy for me when I was building my own site.