Anyway, on subject.
Long-term Paranoia is very doable, but it takes some work. If your players are used to Classic or (ugh) Zap style, it'll take extra work. Here are my three big suggestions:
1) Non-lethal responses for failure, insubordination, and mild treason, including that pointed out by other players. Draft up a long list of punishments that are annoying and entertaining, but also reasonable. A shock collar that punishes people for speaking out of turn, or the confiscation of property or living quarters, that kind of thing. If one player uncovers anothers' treason, give them a bonus taken from the traitor - the ability to control the shock collar, for example. Make it clear that abuse of this privilege could lead to the situation being reversed.
2) Big rewards for corruption and secrecy. In the first mission, make sure that the main quest is as difficult as usual, but that there is at least one easily-accomplished way to game the system, and provide some relatively simple secret society missions. When players complete those missions, give them benefits. Make sure that they start equating their secret societies with "getting stuff done" and "success" while being aware of what an immense pain Alpha Complex is. Positive and negative reinforcement should have them not caring about the mission but caring a great deal about their only source of useful things pretty quickly.
3) Missions and obstacles that are immensely frustrating, but rarely lethal. Since the game's going on a while, you don't want people to die too much. This also allows you to introduce long-term penalties such as a broken leg or the like that will actually matter. Give out equipment and property, and then ruthlessly break it. Keep the players cycling near death, but don't generally kill them. How often they die should be based on how long you want the game to run. ;)