The way to protect classified information and/or equipment is to maintain control over the area where it is stored.
Blow up WTC 7? Now you have to sift through all that rubble to get to the classified stuff. There is all that debris that make it hard to find stuff and makes it dangerous to just wander around. A lot of the classified stuff may not be recoverable has been damaged to varying degrees, or is floating around the area (not the site) having been blown clear during the collapse. Good luck accounting for it all. It is also hard to control a site where everything is scattered around and god knows where. You'd have to post guards, which would be pretty obvious, just to keep unauthorized folks from picking up a classified document or equipment or pieces thereof.
At least if WTC 7 was still standing, you can enlist the assistance of NYPD in securing the classified stuff. They'd be more than happy to help preserve national security. The building is more easier to secure and you know where the classified stuff is. No need to hunt around the rubble to find it.
So, again, why blow up WTC 7?
I think the above also sort of deals with the idea of demo teams on standby just to do things like blow up WTC 7. Hmmm, note that the demo team is intending to blow up the building not do a "controlled demolition". You destroy the secret stuff by setting the charges on it, not bring down the building hoping that the collapse destroys the secret stuff.