We recently received an update from Google Webmasters via their Twitter feed about Joomla websites being compromised. Threats like this are all too common for websites built with open source content management systems like Joomla and Wordpress. This is one of the reasons why we build custom built websites. Open source content management systems will always be vulnerable to attacks like this, whereas if your code is private your site will be far more secure.
Many companies come to us and request that we buid a site in Wordpress. This is why we don't!