If you have compliance reasons motivating this need for encryption, you'll find that e.g. HIPAA and PCI-DSS ignore technical reality, in favor of requiring that you encrypt information stored at rest and imposing substantial penalties on you if it leaks. There are a variety of ways to do this. One fairly common one for HIPAA-compliant applications is putting the e.g. MySQL data files on a partition which is block-level encrypted. You then issue decryption keys to folks who need them, such as e.g. the application.
If your host is totally compromised, the host holds both the decryption key and the ciphertext, which means "Sucks to be you." However, this does provide non-zero increase in security (e.g. if an old copy of the DB drive ends up floating off to eBay because of poor physical control on your part, and you can document that it doesn't include the encryption key, you just avoided a reportable information breach), and it does check the appropriate boxes on e.g. HIPAA.