As written before, rsync will not delete from the source, only on the destination.
In your case, I would generate MD5 hashes of the files on the mirror server, then check on the primary server if the hashes are correct and remove those files.
mirror$ find . -type f -print0 | xargs -0 md5sum > mirror.md5
..transfer mirror.md5 to primary server...
primary$ md5sum -c mirror.md5
Check for any FAILED files, then remove the files that have been transfered succesfully. You could automate it like this:
md5sum -c mirror.md5 | grep 'OK$' | sed -e 's/: OK$//' | while read FILE; do rm "$FILE"; done
This will filter all files with a good hash, chop off the 'OK' part from md5sum and remove the files one by one.
Needless to say, after this you don't want to use the --delete option from rsync to transfer the second half of your files...