If somebody managed to hack into your servers deep enough to access private keys, you are f*cked anyway (they can as well delete/encrypt all data), so it's not an argument against user data encryption. Actually, storing private keys safely is easier than bulk data, because you can use dedicated hardware for that - HSM.
We've just hacked your server and wiped the crypto keys for your users. As you know, all your backups are now useless.
Send us $1 million in Bitcoin to get your crypto keys back.
Sincerely,
Hacker McHackface