MSconfig is absolutely the wrong way to go about disabling services.

If you disable services through MSConfig, you essentially wipe them out of existence from the rest of the operating system. This means if you screw something up, it won't be salvagable without a system restore or a third party tool.

However, if you use services.msc(which is available on Win2k and 2k3), Safe Mode can still be used to start the basic services and fix whatever went wrong.