Hi.
I also would like to know HOW to manually unpatch the Joomla index.php.
I would unpatch it with JSMF but it gives a rather interesting error: "Can not find file", even though it clearly detects the file as beeing patched... cool huh? Same for the sms files. I only care for the Joomla instalation to be unpatched.

Reason I want to unpatch: I want to delete JSMF as it is not compatible with CB captcha plugin. I couldn't find any fix, so...
Hope you'll fix this later on.