At the beginning of each mission you will start out with a silenced pistol and the enemies will be unaware of your presence. Sneak up behind them and kill them with one headshot from the pistol. You must make sure the icon on the radar is Green for this to count towards the 50 required. Yellow or Red dots do not count.
You should be able to get 4-5 this way each mission. Since you have to play the game 3 times you should get this halfway through your 2nd playthrough. If you are impatient, just keep replaying the first part of mission one and you can get 5 or more kills each time.