I don't claim to be a security expert, but I have ran a server for a number of years. Keep in mind that whatever you do, running a public a server on the Internet is always going to put you at some risk, known security issue or not.
You're already making daily filesystem and mysql backups, right?
Just a cursory inspection of that list of functions, you're going to run into problems when Craft uses the filesystem, for example uploading assets, renaming files, etc. You should probably leave out:
move_uploaded_file, chdir, mkdir, rmdir, chmod, rename
The intention there a malicious attacker can't upload a file, move or rename it, and then execute it.
Craft already does an adequate job of filtering out nasty files so they don't get uploaded. If you want to go further, I'd recommend disallowing PHP to actually run code in any of your asset upload directories since those are probably going to be above the web root.
I just did a search of the rest of the functions;
phpinfo is used also used the control panel. I don't think that poses as much of a threat. Even if an attacker knows some file system paths, if it he can't write to them, he's DOA.
I'm also a fan of open_basedir. It's a cheap form of "jailing" the web application inside a specific root. I run PHP-FPM which you can setup per pool, per user to make things a little more secure as well.