I would love SWORD to show up and Brand along with it. In fact THAT should be a priority on the SHIELD show, not the "mystery" of Skye. Have Coulson tracking down missing long time SHIELD agents and assets, most dating to BEFORE the unraveling of HYDRA inside SHIELD. BOOM... Turns out that Fury had one last secret he didn't even share with Phil. A secret adjunct organization that was formed to observe and asses non terrestrial threats. Thanks to some true psychics on the team (another secret Fury kept from Phil, along with the confirmation that Thor's landing was NOT the first otherworldly contact certain parties on the planet are aware of) SWORD was never infiltrated by HYDRA, but didn't get involved with things since their mandate is not to get involved with international politics, but to be the first line of defense to keep the human race safe. SWORD can have been formed shortly after Fury started to work on the tesseract, as it was obviously not of this world.