In GWT, provide up to three email slots for us to fill in. When you find malware on our sites, send out an email immediately listing all pages that you believe are infected. Give us at least 72 hours to assess, and to fix.
If the issue is not addressed in that 72 hour period, then REMOVE THE PAGES out of the index. It is wrong to place a label on our entire website generalizing that the entire website is bad.
There is a lot of liability here on your assessment. This label can have devastating effects on the reputation of our sites. And all of this not due to our intentions.
Realize there can be websites who monitor this kind of activity, publish a list and that list will stay permanent in "complaint board" type pages. Those pages aren't going to go away and your reporting of it makes it even worse on website owners. This, including our competitors can use this information against us. This is an extremely important point because now these pages and reputations will be permanently marked.
I hope that your team will be fully responsive over this issue and turn around and remove the flag quickly. Every person who searches through our sites has potential to be turned away for every minute you fail to process our response. For ecommerce sites, this would serve as terrible PR and may also leave long lasting damage to our businesses.