I've played several games that have used such a feature as this, and it's always been a sore point for the playerbases in said games. Brink won't be any different.
**The only ways to counter scrubs who spam this ability will be to either waste ammo into teammates (1st technique), play as a class that can detect enemy players using such an ability, or narrow your battlefield focus down to looking for the subtle queues and actions that distinguish an infiltrator from a real friendly (3rd technique).
**Yes, there are only three ways, and perhaps that's enough, right? Wrong. Each of those detection techniques have serious drawbacks.
--1st technique will leave you wasting your ammo supply, while at the same time needlessly revealing your location to the enemy if you're not using an undetectable firearm.
--2nd technique has the unfortunate side effect of creating what is classically defined as an "overpowered" player class/loadout/carreer option. More people will use the class in order to spend entire rounds just sneaking up on enemies for kills. More people will use the class in order to easily spot enemies who are using it. And again, back and forward, back and forward, until this class is spammed all over the battlefield with more and more players paying little heed to whether or not their team wins the battle. PvP games will increasingly become melee-fests, and campfests. Eventually, any semblance of team-oriented strategy and winning tactics will have to be "FOCUSED" around the possible presence of an abundance of disguised enemies.
--3rd technique, in most situations, is a sure way to get yourself killed and narrow your battlefield contribution down to almost nothing. Alternatively, you will find yourself camping a lot more than usual, attempting to get a good look at any potential infiltrators before they can become aware of your presence. Of course, any gateway to camping is never desirable in such a team-oriented objective-based game.
You missed a few.
The ones with less drawbacks, and the ones the game will most encourage.
4. Let the Operative open fire and as soon as they start shooting, dodge. When they do ANYTHING except move, they lose the Disguise instantly.
5. Equip "Combat Intuition" - an early unlock Passive universal ability (once equipped, will always be active NO MATTER WHAT CLASS YOU PLAY AS). This gives you a visual warning when you're in an enemy's sights. If the only person in line of sight is a teammate, giveaway much?
6. Trust the player who's been used for the Disguise to reveal him.
Given that we have no confirmation of any class being able to see through Disguises, should help.
Also, with the rest of your post, you complained about how everyone will be one-upping and focusing on the Operative as the Disguise class. Unfortunately, you're missing the fact that kills are nowhere near as valuable as objectives, and focusing on those should keep your team ahead of the Disguised players anyway.