Hm. Interesting that your thread and
this thread should appear simultaneously - perhaps some of Kristine's comments might be helpful to you even though the other person had a different experience.
The one and only time my host's servers were hacked (that I know of), the problem was just as you describe - they overwrote my main index, and a rebuild restored everything to the pre-hack state. If that's what happened, I would be concerned, but not overly so -
overwriting the index file is a possibility, but it's not a vulnerability, just something that could happen to any site, MT powered or not. MT actually has measures in place to prevent visitors from entering code in your comment fields, for example, that would cause scripts to execute - that would be a vulnerability in the software.
I hope this helps -
Donna