Leechprotect won't get disabled just be disabling it from feature manager. You can use following steps to remove it completely from your cpanel vps.

Edit /var/cpanel/templates/apache2/main.default

nano /var/cpanel/templates/apache2/main.default
delete..

[% IF file_test('f', '/usr/local/cpanel/bin/leechprotect') -%]
RewriteEngine on
RewriteMap LeechProtect prg:/usr/local/cpanel/bin/leechprotect
RewriteLock /usr/local/apache/logs/rewrite_lock
[% END -%]
Save and exit nano.

Edit /usr/local/apache/conf/httpd.conf

nano /usr/local/apache/conf/httpd.conf
Delete...

RewriteEngine on
RewriteMap LeechProtect prg:/usr/local/cpanel/bin/leechprotect
RewriteLock /usr/local/apache/logs/rewrite_lock
Save and exit nano.

Kill the leechprotect process and restart mysql service.

kill `/sbin/pidof leechprotect`

service mysql restart
Run /usr/local/cpanel/bin/apache_conf_distiller --update

/usr/local/cpanel/bin/apache_conf_distiller --update
Restart apache service.

service httpd restart