I've double checked the PowerPress zip files hosted on WordPress.org, where we distribute the PowerPress plugin from, there have been no cases of malware found. WordPress.org does a great job of monitoring all of the plugins for malware and viruses.
The malware was most likely added by scripts that were uploaded to your web site, usually through a vulnerability with either an outdated version of WordPress and/or some other web server or web application vulnerability. Could have also happened if you installed a theme or plugin from an unknown source (I only trust plugins and themes from WordPress.org). Either way, you need to contact your web hosting provider to see what they recommend, the hosting environment dictates how secure the server is.
Malware and server security is not a function that themes or plugins are supposed to deal with, this is specifically an issue you need to consult with your media hosting provider.