Especially on a larger map, keeping your pretender someplace unexpected (certainly not the capitol) can help, as can having several lab locations with good patrollers, and other locations with good patrollers (fliers, Watchers, etc), to catch spies. Domes are good. Being underwater can help. Rainbow pretenders can often script some pretty effective anti-assassin spells, and keep strong bodyguards... though patrols and other leaders in the same province can really cut down the odds of an assassin getting even that far. If you've got a Robe of Invulnerability... that's generally a good thing.
PvK