I recall several occasions of having to use a CLI to finish the removal of an older anti-virus system (Norton/Symantec/whatever the hell they are now) to upgrade to either the business edition or just to a newer, more "feature"-laden version. It also involved hacking through the registry. I seem to even remember it being a case of Safe Mode, Task Manager, kill a few processes, delete a file or two, remove some registry entries, run a removal tool from their website, reboot, remove the rest of the files manually.
This problem existed for enough people that they had step-by-step instructions on their site. And before you ask, these were XP machines (after Windows 2k) and were otherwise in perfect working order.
Now, it isn't Microsoft's fault that anti-virus software tends to run in a manner similar to the problems they are supposed to remove, any more than you can blame "Linux" for the problems certain packages have with setup.
Anti-virus software has most likely caused me more headaches in fixing other people's systems than almost any other software out there, and it invariably ends up with registry tweaking.