This is not a big privacy issue
The internet is composed of some few websites / web applications using self hosted solutions with fully personal servers (owned and operated in their own NOC).
Everyone else is using some form or another of shared, virtualized, semi-private, semi-dedicated, collocated hosting. In every case the hosting company has full access to everything, they have physical access to the servers -- no amount of protection can help you there.
Shared hosting might be the easiest to access from the hosting company's perspective. But that's not relevant, their policies should prevent them from operating in bad faith because if they wouldn't it wouldn't really matter if it was the easiest or the hardest to access it would only matter how interesting the data you have is to them (or some random employee of theirs).
Finding a solution to the above non-issue
Some approaches might use:
- Mounting an encrypted filesystem as a folder and setting up MySQL to use that folder to store its data;
- MySQL encryption functions to encrypt the data in a particular cell or column;
- a library on top of SQLite that had an encryption feature which would encrypt the entire database file;
On the other hand if your PHP files would be on the same server and the database decryption password would be stored inside your PHP files, any "intruder" could find it and use it if they wanted it.
You'd have to store the password on a different server or obtain it from the user in order to not have it present inside the local PHP files. This would obviously still be available at runtime; if the "intruder" is a programmer he will be able to retrieve it fairly easily.
