I know exactly how you feel, this is my first playthrough and I came across the same situation a few days ago, flying bats came and wiped out my boar herds and most of my wolf herd, even after I thought I'd secured the wolves but they found a big enough space to fly through, luckily I had them partitioned and some survived.

It left me feeling lousy though, I've grown used to the relaxed farm atmosphere and the last thing i wanted was my animals secreted away in hardened bunkers.

I'd progressed to having already killed Bonemass so my solution was to make a new world, yea start over, but my plan is to only kill the bosses in 'world 1', while I play without raids in my home world, 'world 2. It's working so far, I recently killed Eikthyr in 'world 1', went back to playing in 'world 2' and haven't had a single raid so far. I have both Moder and Yagmuth marked on my map in world 1 so I'm all good.

Hope that helps, there's a thread of mine a few days ago with some good answers, maybe you'll find it helpful, although I think blprice61 comment just before mine has one of the best answers I've seen.

Honestly, it wasn't the bat and wyvern raids that made me start over, it was a factor, but it was really the 'wolf hunt' events. I can live with the base raids but those hunts are spoiling my game too much and doing it this way may solve both, we'll see...