There's a mechanism in Windows that hooks the boot process to load certain drivers or other critical system processes at startup. If the computer is infected with a rootkit, it likely does something of this nature to reconfigure the Windows kernel to do the rootkit's bidding.
Depending on how this is set up, deleting the associated files doesn't cleanly remove the malware, but instead leads to a STOP error (blue-screen) at boot-up resulting in an non-booting system. Most likely, this malware will inject itself into the "last known good" and "safe mode" configurations as well, meaning the only way to "clean" the system would mean using an alternate boot disk and painstakingly untangling the resultant mess. The level of expertise this requires to do correctly is somewhere on par with "highly experienced Windows kernel developer."
While it's not, strictly speaking impossible to properly clean a heavily infected system, it is extraordinarily difficult, error-prone, and usually far more expensive then just starting over from scratch.