Adrian,

Have you been able to identify exactly which files have changed and the
differences?  Do you have your files source controlled on your end?

You cannot know anything malicious has happened until you can identify
a change which intentionally caused the site to break.  Something like
"this website owned by [hacker name here]" would show up on your pages
or at least be noted in the files on the server.

It could be possible that a file just became corrupted or an upload by
someone placed files in the wrong location which caused the unwanted
result.  If it was just human error, consider scripting your deployment
process.  Look into MSBuild to do that.  If you do have Remote Desktop
access to the server I suggest uploading all of your files at a zip
file and unpacking it in place to ensure you have all of the files you
needed.

I wrote this series on MSBuild which may help you out.

http://brennan.offwhite.net/blog/2006/11/30/7-steps-to-msbuild/

Brennan Stehling
http://brennan.offwhite.net/blog/
ASP.NET JAD (Just Another Developer)