The whale territory dynamics is not quite known for many players beforehand as it's so much determined by how the community plays. I think it's a tough job technically speaking to avoid this phenomenon once you lift the level limit so high to lvl 200. If Funzio did it gradually with 25 lvl increase things may be very different.
To be frank, I would have been in your position as I don't play CC or MA and knew nothing about whale. I'm just lucky to start early and hence avoid the whole hassle. Trust me, you're not in the worst position as you just step into the territory and got hit a few times. I have a few juicy boys who tried to take revenge on me and now become my daily regular feed. I somehow feel sympathy that right now Funzio allows at least 2 * 20 attacks every 24 hour. But hey, who knows when Funzio would change the algorithm and fingers crossed that we don't go back to the dark ages with 5 attack/24 hr limit!
Btw, don't forget to try making friends with whales!
Answer for 12/24/48 buildings: as I said you're not the juiciest of all in a way that you don't really feed well for tourny points and most likely attack on you for exp would inflict some loss on the whales. Unless the whales just want to kill without consideration of cost (yup, there're those kind of crazy whales), most likely only raids on your high input 12/24/48 hour building would justify the cost of attack. Also don't forget that when whales hit you they give up 1 attack to do it on others, so small improvement on yourself can sometimes create huge impact.
Btw, if you leave your 12/24/48 building cash lying around that also leaves an impression that you don't play often and hence an easy prey.
Hope this helps.