Let me preface this by saying your place is absolutely gorgeous, and I love yurts! We have a small one from The Colorado Yurt co. that we take for long camping. Seriously, I'm trying to talk the hubs into a Canada road trip now, just so I have an excuse to book with you.
Regarding the charges- you said you didn't usually rent the yurt seperately, so technically you only lost what time and amenities you put out for them. Were they otherwise good guests? If so, maybe send them a money request, but for a percentage of the normal fee, just to cover the extra effort you guys went to. Tell them you don't want to charge the whole fee, since it wasn't used, and you're just charging for the service cost. You guys recoup what you put in, they get a nice discount, and hopefully everyone walks away happy.