Same thing happened to my guild last week - quite an inauspicious start to war for us, as it was our first war week together!
I agree that the game shouldn't just allow you to deregister the entire guild for the entire week based on opt outs - that's a ridiculous, poorly-thought out solution that GREE added to Guild Wars during the period in which they were trying to fix an exploit in war where some guilds opted out members prior to tough battles to increase their accuracy and crowns gained. It basically gives any member in the guild the ability to deregister the entire guild - all they have to do is be the member who opts themselves out and brings the total below 50% of guild membership or 10 opted in members. It was shortsighted, out of control of ranked members, and unnecessarily punitive at the time, and now that they FINALLY figured out how to handle the exploit that prompted the terrible "fix" (random matchmaking and every opt out offensive battle equals one opt out for defensive battles, too), this rule needs to be removed - there's no point to it. I was part of a council of players advising GREE on addressing issues with the app, and they straight up ignored us while we told them how to fix it.. very frustrating to see it took them months and months to come around to our solution.
There's more to this than unintended consequences of the less than 50% / less than 10 opted in rule - there is also a bug where if your guild is set to "Application Only", any officer, champ, or even the GL who accepts an application will be silently opted out of defence (but apparently not offence). This counts as one less member opted in - EVER THOUGH THEY'RE MARKED AS OPTED IN IN THE MEMBERS SCREEN. So it's possible this may have come into play, too.
The woefully inadequate workaround right now is to set your guild to "Open", and tell members not to opt themselves or any other members out unless they check with you first... not exactly a solution, but if your guild is tightly managed, it might work for you.
As for compensation - we're still waiting on ours. We lost out on rewards completely, and Customer Service has not replied to my tickets or emails for over a week. I hope you have an easier time dealing with CS than we did. Very disappointing that a company has a bug existing in their codebase for years under their control, is unable to fix it, perhaps even unaware of it, and on top of that, CS won't correspond with or even compensate the guild members in a timely manner.