You can do it any way you want but in general in the game, you want to avoid taking on groups of people really. If you go at night, you may find he's asleep and so you can creep over the rooftops to get at him in his bed, avoiding a lot of the guards. They're also much slower than you so my preferred tactic for those sort of areas is to lure a few in, run away across the rooftops and then shoot them with arrows from a distance. Get yourself a decent bow and it's much easier. You don't need to empty the compound of everyone though by any means. You do need to get next to the body and 'confirm the kill' which takes a couple of seconds, so you'll not manage that if there are guards hanging around his body, you'll need to kill them.
Firebombs and sleep darts are your friends in this game, the sleep darts especially, they'll put near enough anyone to sleep leaving you an easy kill.
