Corrected entry: At the end, the suggestion to unplug W.O.P.R. to prevent the missiles from being launched was actually the right suggestion. Given that W.O.P.R. was guessing the launch code by brute force, the actual order to launch the missiles wouldn't be given until the launch code was determined and therefore the silos would not interpret anything until they received not only the order to launch but with the right launch code.
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Correction: This was explained in the movie. Unplugging W.O.P.R. would trigger a failsafe that would launch the missiles automatically without needing the launch codes, on the assumption that the disconnection meant NORAD was no longer operational. Given all the ways communications could be interrupted this is a stupid failsafe but, in the context of the movie, this isn't a plot hole.