flash bios off a new image and then replace hard drive and format from a cd.
All of this is going to get worse because of the way that current OS implement the kernel. Even linux is vulnerable to this kind of attack . The problem is the mindset that some programs need to be admin or root to install . Once those programs have admin/root access nothing watches over the program to see if what it is doing is secure. A program can claim to be installing itself but then also look around on the system and change other programs.
The fix is some of the newer approaches to OS design that make it so even with full admin rights one program cannot see anything outside of its own domain. So even when installing a program that program can only see the folder it is installing to, it can't access windows, program files , documents, or anything else. It is essentially locked in its own virtual machine without the ability to change anything on the system except what is in its own root folder.
The current OS models are old, forged 20 years ago, and have been patched over and over to try to fix the problem. Sometimes you just need to start over.
A good read on one of the new OS frameworks.
http://genode.org/home-page/documentation/general-overview