From the Devs:
You can also use the /guild command to modify the values without going through the UI, like this:
/guild rank_permission 1 0 False
This would remove invite permission for rank 1 (senior officer). Here's the full documentation:
guild rank_permission <RankId> <PermissionId> <True | False>
PermissionId is:
0 = INVITE
1 = KICK
2 = PROMOTE
3 = DEMOTE
4 = PATRON
5 = DEPATRON
6 = MOTD
7 = RANKPERMISSIONS
8 = RANKNAMES
9 = SEE_OFFICER_NOTES
10 = EDIT_OFFICER_NOTES
11 = SEE_OFFICER_CHAT
12 = SAY_OFFICER_CHAT
13 = SEE_GUILD_CHAT
14 = SAY_GUILD_CHAT
15 = EDIT_OWN_NOTES
16 = EDIT_OTHERS_NOTES
17 = EDIT_EVENT_FILTERS
18 = EDIT_EVENTS