UPDATE: I now recommend using WfpDeprotect, also a free utility by us, which will deprotect files and folders for 1 minute, allowing you to do whatever permenant operation you wish on them during that period.
WfpReplace will replace a WFP (Windows File Protection) protected file without having to boot into safe mode.
WfpReplace is a console mode utility that works just like the 'Copy' command.
WfpReplace is FREE, but donations are encouraged if you find this software useful.
Also try Process Lasso, our free process priority optimizer.