It is not possible to set sub-if down while super-if is up.

Initial state:
lab@BM:~$ sudo vppctl show interfaces
Name Idx State Counter Count
GigabitEthernet0/8/0 5 up
GigabitEthernet0/8/0.10 8 up
GigabitEthernet0/8/0.20 10 up
GigabitEthernet0/9/0 6 down
GigabitEthernet0/9/0.10 9 down
local0 0 down
pg/stream-0 1 down
pg/stream-1 2 down
pg/stream-2 3 down
pg/stream-3 4 down
vxlan_tunnel0 7 up

step 1: set GigabitEthernet0/8/0.20 down
lab@BM:~$ sudo vppctl set interface state GigabitEthernet0/8/0.20 down
set interface state: super-interface GigabitEthernet0/8/0 must be down

Expected result:
It is possible to set sub-if down while super-if is up

Result:
It is not possible to set sub-if down while super-if is up

Version:
lab@BM:~$ sudo vppctl show version
vpp v16.09-rc0~42-g750c625 built by root on BM at Wed Jun 1 07:11:20 CEST 2016