That's the underlying, fundamental, question...
Is it the "loose cannon" character (PC) that's causing the problem or is it the player him/herself?
Basically, for me as the GM, I get to know "everything." So if a player wants to play a loose cannon (or a backstabber, or an assassin out to get another player, or a mole in the team, etc.) then they have to run it by me, let me be privy as to what they want to do/accomplish, so that I can weave it into the overall story of the game. And with playing any of those parts the player gets told, "this is going to piss off other players, not just their characters, so we better have real good reason for introducing it." Where "good reason" explicitly means, "it's going to be a hell of a lot of fun for everyone when the story plays out."
Look at every good action movie. If there is a loose cannon in the movie then he (typically male characters) is either the protagonist, the single hero of the story who has to go his own way to get the job done because the other good guys are either too inept or bound by the laws, rules, etc. If it's not the protagonist the hands down it's going to be a "crew" movie and the loose cannon becomes a minor antagonist who throws a wrench in the heroes plans and in the end...he has to die. Critical Bill from "Things to Do In Denver When Your Dead," Waingro from "Heat," Gregor from "Ronin," all fit the loose cannon/backstabber role...and a loose cannon in a crew film is bad for the crew and lethal to the loose cannon.
If it's the player (regardless of the character they're playing), then that's a whole different issue. In the end it comes down to you can give them a warning/choice to either be a team member, be a loose cannon with the above GM controls, or stop playing.
I had one player once who really just wanted to hang out with everyone, but would have rather gone out drinking than play an rpg. He didn't express this to me. The group spent two game nights coming up with backgrounds (all UCAS military black-ops inserted into Seattle to be used as the military saw fit during the Renraku Arcology shutdown). I wrote up a detailed "briefing document" on all the issues they may face. There was a lot of effort put into this by everyone.
Then the first run: Find a decker, bring him in for interrogation. The team found where he lived; in the second story apartment of an old converted Victorian in Bellevue. The trouble player (who no one was aware was going to be trouble yet) and another team member head in, up the stairs and station themselves outside the door. The other players were outside, watching for an escape. The two inside break down the door, flash grenade, then rush in. The trouble player heads to the computer room, while the other player heads to the bedroom. In the bedroom the other player notices a fireman's pole in the closet, with a locked "manhole" like portal in the floor, and radios the information to the group. The trouble player notices that the decker's "computer desk" has video feeds coming from security cameras outside, and that there is a timer, counting down, 7. 6..., "One action left, what do you do?" I ask the trouble player (there was still one more round after the current one before the bomb was going to go off). "I run out of there," he says. "Do you say anything to the other player?" I ask. He says, "no." Do you use your comlink to let him know anything? It's just a free action, you have those." "No." Trouble player makes it out. With the info about the fireman's pole from the other player, the rest of the team focuses on the first floor and find the decker sneaking out. Just as the other player gets near the door to exit the apartment (he stayed in character, didn't act on information he didn't have)...boom.
Later I talked to the player, found out he was just in it to hang out. So we decided to hang out on other nights.
The only thing a loose cannon can hit is team morale. (at least non-GM sanctioned loose cannons).
