Are there any tools that can override what a malicious virus/malware can do when it stops processes

Here is an example. I had someone who had something called I believe "Internet Security Pro" Everything I had attempted to transfer and installed was killed by this including NPE. I had to have the user take the PC off of the network and run NPE in order to remove the garbage. What I would like to do is kill that process and NOT permit it to restart but no matter what I did, that things kicked off the dirt, came back on and contunued to wreak havoc. Since we are in different sites, going through Safe mode is not that good of an option.

Any ideas, suggestions ?