If the database still exists, it will probably complain about missing files, but that’s not a huge problem. Assuming the local system (and its database) got destroyed, you’d be doing a direct restore anyway. Make sure you have an export of your job configuration stored somewhere else that you can rely on.
Defense against trojans is basically the same idea and might be simpler than on tape or cold storage (which you can search forum for, e.g. Glacier), because I assume the remote files would be readable.
You might want to make maintenance windows possible, e.g. to clean up old versions before backup and database get too gigantic. There can also be times when problems may require changing remote.