...destroy stuff just for the heck of it... it does this only if the particular program or dll is infected with any trace of malware or spyware, etc. You also have to follow the instructions to the "T", like for example it SHOULD only be run in Safe mode, but if you walk away and it reboots the computer to go to a different phase, and you are NOT there to force start in safe mode, then ComboFix will do unexpected things.
So here is a catch 22, If you want to put ComboFix together with all your tools, be careful how you use it, if you are worried that it will destroy half the programs installed, then don't carry it.