It can be done entirely over FTP if really necessary, just requires a few more hoops to jump through:

-- remount rw: site rw
-- rename the existing /empeg/bin/player to something else
-- make a new copy of it under the original name
-- chmod 755 on the new copy (original name)
-- delete the original (now renamed) file (yes, you can do that even while it is still running)
-- patch the new one (original name)
-- remount ro: site ro
-- reboot: site reboot

Cheers