The MSRT (that is the common short name for the tool you are talking about) was created due to a rash of Blue Screen's of Death that happened after windows updates a few years ago. These BSoDs where caused because malware had hard coded hooks in to kernel DLLs, when these kernel DLLs where updated the addresses changed and caused the blue screens to happen.
Because people started getting upset at Microsoft and where getting bad PR for "Windows Updates causing blue screens" they started releasing the MSRT and have it run a few checks during the update process to ensure that no malware was installed that would cause the reboot after a windows update to blue screen.
The MSRT is not a anti-virus IMHO, think of it more as a "integrity checker" to help windows updates know it is safe to modify system files without crashing the computer.
(I don't have any direct sources to quote to back up my statements, I think I remember hearing this from a Security Now podcast but am unsure which episode it was.)
As for worrying about slowing things down, the MSRT is not a constant scanner like most AV software. It will only perform a "quick" scan after the first reboot after updating itself (updates come out once a month), however you can also do a manual full scan by running mrt.exe
manually from a run dialog at any time.