This inspired me to try this:
# show interfaces ge-0/0/0 ge-0/0/0 { unit 0 { family ethernet-switching { port-mode trunk; vlan { members all; except NATIVE_VLAN_NAME; } native-vlan-id NATIVE_VLAN_NAME; } } }
you have to use the name, not the vlan-id.
I cannot find it documented anywhere, but it works for me (EX2200-C-12P, Junos 12.1R3.5 , 12.3R12.4 and some 14-version).
Hope this helps!