Take your website offline
If your pages have become infected with viruses that will attack your site visitors, which is usually the case, you should protect your visitors, and your reputation, by , which involves adding a few lines to your .htaccess and optionally uploading a file. If you do this right away, you might avoid getting the "This site may harm your computer" warning in Google search results and a similar warning at Yahoo.
Are you hesitant to take your site offline? Consider this: a visitor who finds your site down will hardly notice the incident and will (or at least might) come back later. A visitor who gets attacked by a virus from your site will develop a strong memory of the incident and probably not come back, ever.
In addition, it is possible that a script with a security hole was the reason the site got hacked. As long as that script is publicly accessible, the site remains vulnerable, which means it could get hacked again even while you're trying to repair it.