Another option would be to use Sukhozin. You could at least limit exactly where the system call can and, in turn, restrict access to this directory.
Here is a basic vhost.conf configuration example where shell_exec is locked everywhere in your domain except for ffmpeg-folder using Suhosin
<virtualhost *:80>
ServerName your.server
DocumentRoot "/var/your/public_html"
php_admin_value suhosin.executor.func.blacklist "shell_exec, passthru, show_source, system, pcntl_exec, popen, pclose, proc_open, proc_nice, proc_terminate, proc_get_status, proc_close, leak, apache_child_terminate, posix_kill, posix_mkfifo, posix_setpgid, posix_setsid, posix_setuid, escapeshellcmd, escapeshellarg, exec"
<Directory "/var/your/public_html/ffmpeg-folder">
php_admin_value suhosin.executor.func.blacklist "passthru, show_source, system, pcntl_exec, popen, pclose, proc_open, proc_nice, proc_terminate, proc_get_status, proc_close, leak, apache_child_terminate, posix_kill, posix_mkfifo, posix_setpgid, posix_setsid, posix_setuid, escapeshellcmd, escapeshellarg, exec"
</Directory>
</virtualhost>