Plasma rifle has it's purpose as a long range assassination weapon against a target with it's shield off. Problem is, you need the target to stand still or move in the same direction as your shot goes. A missile launcher is eventually attracting attention, whereas if you score a hit with the plasma rifle it's a clean and quite silent kill.
As a combat weapon plasma isn't that good long-range, I've seen it often enough that one can just step aside to avoid being hit. I see it mainly as an assassin weapon sniper style and being undetected - score the hit, get a clean kill and leave the area. Mission accomplished. At least that is how I would do it, when the target isn't in a building.
As far as close quarter assassination goes, I ask myself, if one can do that whilst being scanned - if it is possible to kill them while they are busy scanning. It is something I tend to do in assassin's creed games, get the attention of someone, close in quickly and drive my blade through their guts or wait around a corner and kill them as soon as they show up. Not fight them, but kill them right away - not letting them any chance. Is that possible in EDO during being scanned by them?