Yes, instead of having a server upload backups to another, get a server that connects to the first and runs a MySQL routine daily.
For example, with Windows servers running MySQL, you can use SQLyog as a Windows task scheduled daily. The web server has no access to the backup server. The
The backup server doesn't even have to be a server that's online for web. And you can use a number of really secure login methods -- port knocking, alternate ports, different user/pass from the web server you're backing up, IP locked to a single system, etc. That way nobody can really get into the backup server. The more open (and not quite as secured) web server may be at risk, but the data isn't.
Just a security 101.
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