My initial knee-jerk reaction was "Crap! The Diedne had the right idea...let's go to the Magic Realm and hide until the Resurrection!" But then I stopped panicking and started thinking about it.
I think the main thing we have going for us is knowledge. We now know the truth about Guernicus and the history of the Order...or, at least, we think we do – Fiona's still not 100% sure. Everything she's been taught and believed for the last forty years was wrong, and she's basically stripping gears right now. But she'll come around.
So, we know the truth. We know about the Duresca scrolls, even if we don't actually know what's in them. (Do we even have the scrolls? Not sure, I'd have to go back and check). But Guernicus doesn't necessarily know that. They know Apollodorus/Xenophon was a very secretive, cunning, and manipulative s.o.b. It may be possible to convince them that we're ignorant about what happened, that we know nothing about Xenophon or the Duresca Scrolls or anything, that we're all Good and Loyal Servants of the Order and pose no threat to them.
Meanwhile, possibly use the Magic Realm as a "safe house," hide anything and anyone we don't want discovered there while we look for the Diedne. I doubt that we can convince them that we're sorry about what happened...in fact, it's possible they may be "shoot first, summon the shade, shoot it, summon the shade again, then ask questions," but if we can convince them of our situation, they might be invaluable allies.
I'm thinking the fact that we were chosen to host the next Tribunal might actually work in our favour. I doubt that they will wipe out the whole covenant and leave the Tribunal in the lurch, and Tribunal might be an opportunity to make some allies just in case.
I also find myself wonder if (1)the ex Misc Census might be of use to us in this situation, and (2)whether the giants with Parma might have anything to do with this, or if they might be somehow recruited in our coming battles.
"Surreptitia" is her childhood nickname!