I mean the teams are small (8 max) so I dont think itll be too hard to spot someone who is acting weird especially since the characters are super customizable. Plus even if friendly fire is on if you are in a situation where you think someone is a operative a cpl shots will tell you if you are correct and if not then your teammate can easily recharge his health / pip since they only took a cpl shots.
From what I can tell the operatives disguise seems to shine with those who want to be the super stealthy lone wolf who goes after the stragglers / people who are away from their team. I dont see it being as much of a "OMGWTF!" ability as it is in TF2 and KZ3.