I'm not sure...but it seemed like there were always threats from either Division or from the White House...Bill Buchanan at the end of Day 5 thought that Vice President Gardner would shut down CTU...but Karen Hayes, on loan from Homeland, personally suggested CTU stay open, and that Bill continue to run it. (no wonder they got married!)
However, if it was Congress that disabled it, I'd not be surprised...leave it to Congress to shut down something that works...and to subsidize something that doesn't...
Maybe CTU just went underground and Tony still works for them, and it will all make sense that he truly didn’t go to the Dark Side.