Re: Backups
As you point out encrypting (or doing a backup) of a database by attempting to simply doing it file by file will result in a corrputed database [if the files are modified by the database while you encrypt/backup].
If the attacker does it that way (maybe not even knowing the files belong to a database) your data will be corrupted even if the attacker does not tamper with it.
So let's assume the attacker is smart enough to have an encryption process that takes care of those things.
What stops an attacker from modifying the data before starting the encryption process if he has full administrative access?
Restoring the system using the decryption tools provided by the attackers will restore the system to a state where you KNOW it was vulnerable (and includes any tampering the attacker might have done).
Trusting an attacker to not have added a few extra remote administrative access options in case they want to come back is something i would not recommend.
Unfortunately restoring from backup is not much better. Unless you know for sure when the attacker first accessed your systems and you use an older backup you still have to assume the backup contains things you don't want to have. You although end up in a vulnerable state and have to figure how the attacker got access and close that hole or he can just use the same vulnerability to come back.