Cisco outed Barry as the Flash since Snart was torturing Cisco's brother. Cisco made a choice, save his brother and put Barry and his family in danger or let his brother die.
A no win scenario.
Captain Cold is alleged to appear in the pending ATOM spin off but he will still show up in the FLASH at times, I'm sure.
Cold stated he has a time delayed uplink that will send Barry's ID to the world, but Barry challenged Cold and told him that he was good enough to accomplish his goals without killing, and Snart seemed to accept that and agreed to back off, especially after Barry made it clear he will kill Snart and any of the Rogues that come after his family ever.
What I like about Snart is that since day one of his appearance, he has always stepped up his game to compensate for things like the cops and how long they take to respond, then he ups his game to compensate for the Flash by getting the cold gun. After that he ups his game by getting Heatwave and tossing him a heat gun. Now his sister breaks them out of the police van before they reach jail, aids him in getting the cold and heat guns rebuilt then asks for a gun of her own, thus again upping the game.