Has the FAA ever halted flight operations?

Yes.

On September 11, 2001, four flights were hijacked by terrorists (American Airlines 11, United Airlines 175, American Airlines 77, and United Airlines 93), and three of these aircraft were crashed into buildings by the hijackers ( AA11 and UA175 into the World Trade Center, and AA 77 into the Pentagon), and the remaining flight (UA93) crashed in a field in Pennsylvania.

With no way of knowing of how many airborne and future flights were at risk to further hijackings, the FAA took the following steps on 11 September 2001:

• 9:17 AM: FAA shut down all five airports in the New York City region.
• 9:26 AM: FAA issued a nation-wide "ground stop" order, prohibiting all civilian aircraft from taking off.
• 9:42 AM: FAA ordered all airborne aircraft to immediately land at the nearest airport, forcing over 4,000 flights to change their flight plans and land.
• 10:24 AM: FAA closed US airspace to all international traffic, and diverted all inbound flights to their point of origin or to Canada.

The US airspace remained closed to all civilian aviation for two days. On 13 September, the FAA allowed civilian airports to re-open with restrictions and on a case-by-case basis. It was not until 21 September, 10 days after the events of 911, that the FAA resumed all civilian flights without restrictions.