In my attempts to find any plausible reason for what took place during that timeout (when the success of our season could've been decided), this is the only thought that makes sense.  This came from the "In Bill We TRUST" portion of my brain. 

Perhaps he was sending a message he hopes will reverberate for the remainder of the season.  The message is " Despite our talent level, our pass rush REALLY bites. Since you MEN won't man up and handle your business (Burgess / Thomas etc... then I will embarass you on national television".  The deactivation of Thomas could've been just the tip of the iceberg. 

Too bad the "Force" wasn't with us....