Game mechanics aside, as a player you give the assassin the grudging fear and respect that he deserves given the level of threat he presents to you and your friends. As a DM you think VERY carefully about just how arbitrarily lethal you want your game to be. Offing PC's out of the blue with a save-or-die effect SUCKS for the player. I'll repeat my personal, constant refrain:
As a DM you have the ability at all times and in all ways to kill the PC's whenever you choose to have them dead. The game is NOT about simply proving that to be true. Just because you CAN kill them easily doesn't mean that you MUST, or even SHOULD.
Give them due warning that they are, or might be, facing an assassin. It is then THEIR fault if they choose not to take precautions. Any good assassin should know the kind of undesirable attention they draw to themselves when they assassinate someone in open view so they will be mindful of the CONSEQUENCES of doing so. In any case, assassinating in combat requires 3 rounds of observation. This is something that likely can, in turn, be observed - by the target or his friends. If you SEE that you are being studied for assassination you can maneuver to prevent the assassin from being able to reach you.
Assassins in my games generally do what they do FOR MONEY. That is, not just for the change in your pockets but because SOMEONE IS PAYING THEM GOOD SUMS TO KILL YOU. Without that motivation most of my NPC assassins would have to be EXTREMELY upset with a PC before they'd start considering a premeditated assassination by stealth.