-Section 31 confiscated Scotty's transwarp beaming equation.
-Section 31, along with Khan, built the portable one-shot transwarp beaming device.
-Section 31's top secret R&D department beneath London was destroyed. Therefore, transwarp beaming now exists only in Spock Prime's head.
Seems to me that, even of it was a problem (and I say it wasn't), that it's been written out of the Trekverse quite effectively.