In addition to "Bloodlines", there's also "High Ground" where likewise our heroes agree that super-transporters are known to the Federation but impractical and unsafe and therefore not in use. Sounds consistent to me; it seems that ol' Emory Erickson already had it all figured out, but his research proved that super-transporters were not worth the hassle.
Not until Scotty's improvements, that is. Or then Scotty only made the devices a tad less lethal, but that was enough for Spock Prime's purposes of stopping Nero; Spock wouldn't have worried all that much about the personal safety of Kirk at that point.
Section 31 confiscates the equation from Scotty, and builds the portable transwarp beaming device. Khan steals it and beams from Earth to Kronos.
Or Marcus hands over the device to Khan so that Khan can go to Kronos and become a convenient target for Marcus' torpedoes. Khan may be fooled into thinking he stole the device from Marcus against the Admiral's will, or he may be fooled into thinking that his going to Kronos is to some different purpose and will not result in his death. Or then Khan is supposed to be fooled that way, but knows from the get-go how Marcus is betraying him, yet plays along because he also knows how to save his own ass.