We hope to offer malware detection and clean up services later this year. But if its auto updated half way there. My email is Ben@WebPub.com too.
I was wondering if they flag hacked themes only, installations too.
This is also a big reason why we started Webpub.com (startup), it keeps all your WordPress insallations auto-updated without you having to do anything. And soon plugins/themes and other scripts like Drupal, Magento etc. Spent the last year building a framework on the bottom for secure FTP/Web interaction, an XML-API for the middle, and the frontend just launched about 50 days ago.
I've had no complaints with them and if you're worried about this sort of activity you might want to consider switching to use them as a hosting provider.