Using the sniper rifle in a carefully co-ordinated plan to take out the top leadership of the cult in one shot is a great idea if the Acolytes can pull it off. But it's a narrative solution, not a combat solution. If the PC's set up their plan well and roll well (to hit), then there's nothing stopping the GM from saying the Big Bad's head explodes like a watermelon. Conversely, if the GM wants this person to live, then there's nothing stopping him from having the Big Bad dodge, or have a force field, or have a loyal body guard take the hit. These are all narrative elements completely under the GM's control.
If the rules require GM fiat to function in even a half-way rational manner, that's a problem. Even FFG seems to recognize this, which is why the sniper rifle now has the Vengeful quality.