If you're an assassin, you'd probably only be using very specific types of firearms.
Sniper Rifle: Mission would be get to a good spot, and shoot the target. You could have a selection of possible perches for each mission, you'd choose which one, and each one would have different bonuses and detriments. The closer the perch, the easier to hit the target but the more likely you'd be found and the more difficult it'd be to get away safely.
Silenced Close range weapons: Pistols, SMGs and the like. This might be implemented like a modern day cover based 3rd person shooter. I could see the Conviction system working well here, you peek around the corner and tell your guy to hit goon A, B and C in the order B, C, and then A. Maybe the key thing would be killing them in the right order. You're an assassin, so you should be extremely good with tools of death. So the use of auto targeting is somewhat acceptable. If you kill the goons in the wrong order, you might have the problem of dealing with the sounding of an alarm or something.
Rifles, Machine guns: I have no idea how this would be implemented. Maybe just a free for all situation, you have no choice but to kill everything!
I definitely see many possibilities for smoke grenades and flash bangs.
There's always the possibility that guns are not implemented. You could always go for one of two ways for explaining this.
1.) Honor code, a true assassin/templar must kill each other close and personal
2.) Device that makes guns obsolete. Think shields in Dune or something that disrupts the function of guns. A small localized "sciencey" field that prevents mechanical parts from moving or some BS like that.
Anyways, those are my thoughts, sorry it was so long.