I have to agree that it is more often the sound that gives them away than anything else. I've a surround sound set of headphones, and the same instincts to noise that helps me torch Spies in Team Fortress 2 helps me torch stalkers in KF.
And with the flamer, I barely need to hit them to contribute since once they've lit up even if they survive everyone knows where they are and they're quickly put out of their misery.
Hey, here's a terrible, terrible idea. What if there was another enemy that could go invisible? Something a bit tougher if less plentiful that also helps commandos level their perk? it would make a commando more useful since they'd be better equipped for dropping one and could pick it out of a crowd before it's up in your face meleeing you. Maybe make it stronger than a bloat but weaker than a husk. Still a threat, but not as big a deal as an invisible Scrake strength zed would be.