But why not follow RAW?... In my opinion the case of a single assasin attacking a single completely unaware target from hiding is definitely a situation where following the initiative and surprise rules can give a very counter-intuitive result, and my solution is simple; don't roll initiative. The assassin goes first and gets to make his attack. If the target is still alive after that, combat proceeeds normally.
Assassin says I'll snipe Duke Dunderhead from my inn window. Okay, you have surprise, roll initiative, you win proceed / you lose proceed.
Maybe just roll NPC initiative in secret?