I'm checking with admins but normally we don't have the ability to restore deleted files, even if it's from a compromise. The backup type we normally keep would mean rolling the entire server back, which wouldn't be feasible both due to the amount of data and other users who's data would suddenly be rolled to older versions.
The best I can advise for now is if you have backups, you should restore from those. If not, you may end up having to start over; with any luck the rogue didn't erase your MySQL data, but if they did you may have to start 100% from scratch. This is part of why the Terms of Service details that backups are the sole responsibility of the customer; it may seem harsh but no service is free from failure or hack-proof, so the webmaster should always have their own backup for emergencies that require it (even if we have backups, it's usually faster to self-restore).