1. Keep the offer and choice completely private. Don't start the game with the knowledge they are all opposing agents or what not in the open.
2. Allow players to actually be loyal (and if everybody chooses that, well they didn't want spyworks game anyway).
3. Keep the secret part clear. As in discovery with proof has bad consequences.
4. Have some mechanism in place to prevent blind accusations.
5. Look over the Paranoia rulebooks if you can.