Hi Scott,
The plugin cannot take the wesbite down, while it is inactive, it is impossible – as the code does not execute whatsoever.
Do you have any custom code, customization, custom plugin, custom theme code etc.. that may use any of the search functions? That is the only cause I can think of. A custom code may want to access one of the search internal functions or the API, and because it is no longer active, it fails.