Pro tip: Do not give anyone, not even your spouse, access to the guild bank. Or stuff like this can happen.

SE will not restore stolen gil from an fc bank, just like they will not restore a house that was dismantled. From the replies other ppl have gotten about the same issue, SE leaves that up to the fc to safeguard and if you give access to your gil to multiple ppl, you are forfeiting it if its stolen.