Unfortunately this appears to be a server compromise
using the classiic shell script. Could be wrong on that one.
The other option is a compromised FTP login. If the logs were not erased you may be able to see the point of access.

You should be able to replace your index.php file if in fact it was overwritten most likely an index.HTML has been loaded and it would load before the .php file

change your FTP password do not store the password to your computer

ask your host to take a look at see more the server to see if possibly a root kit has been loaded

find out if your site was the only one affected on that server

last effort move to a more secure hosting environment

I would not consider this a problem with the script itself

regards,
DosDawg