webjunk

No. You would not want to do that anyway. Probably could write a script to do it but if one ever fails you will spend a lot longer trying to figure out the problem and hot to fix it.
Been doing it for years, and setup sites all week long and while I do copy several plugins with my WP files, I manually activate each one. Every time.

You can look at it differently if you get a hosting company than can provide 100% of what WordPress needs. But then you have to deal with spending less money for hosting, get much better support & will even at times help with WordPress issues and not state “not supported” like godaddy. Or you can spend hours (which will later turn into days and weeks) trying to fix problems like these with godaddy….

http://wordpress.org/hosting/

It does not sound like an issue with WordPress but elsewhere but if you must:
http://codex.wordpress.org/Hardening_WordPress
There is no plugin to secure yur site. Good practices is what counts.

1)
Have your local copies of the website been alteredd? If so then its happening on your local computer, if not then on your host.
2) If your ftp password is exposed, see if you can use SFTP with your hosting account.
3) Is this Windows or Linux hosting?
4) Is it only your index.php or other php files?
5) Have you gone throug:
http://codex.wordpress.org/FAQ_My_site_was_hacked

http://codex.wordpress.org/FAQ_My_site_was_hacked

Guess you figured it out.

That is called Magic Quotes. The backlashes are added so that the quotes are interpreted as quotes and not part of PHP code.
Check in your theme files to see if they have “add_magic_quotes” in there. That is the WP function to do that.
Also if that did not help, could be your host upgraded to new version of PHP.
look in WP-Settings.php (main WP directory) and look for a line like:
set_magic_quotes_runtime( 0 );

change it to:

if(version_compare(PHP_VERSION, '5.3.0', '<'))
{
set_magic_quotes_runtime(0);
}

Check the plugins
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