The sniper class that kills you unseen from a huge distance is just doing their job. Hating them for that is like hating a shotgunner class for being superior in a close-range enclosed environment, or hating the guy on the mounted gun for being able to mow down waves of infantry. Sure, it's frustrating to be caught on the wrong side of these guys and their specialities, but removing them would leave the game bland or unbalanced.
I have made a point of playing extensively as a sniper in every game I've had since I got a PS2, and I have to say it really is an experience that no other class can match. Both in multiplayer and single, I've found that a decent sniper CAN turn the tide of a battle, and CAN help the other class units effectively. While it might be boring for the guy who gets taken down by an unseen sniper, I suggest that the most cathartic possible solution for them is to experience life from the other end of the scope. There are few things more satisfying in the gaming world than pulling off a successful sniping run: scoring a critical hit on a Badass in Borderlands and saving yourself the hassle of a protracted battle; taking out the campers in a Medal of Honour multiplayer match; hitting that guy on the turret in Battlefront; the immense moment in Gun where you compensate for the reticule to hit some doy cowboy in the head with a bow, and the satisfying squelch when it the arrow thuds into his brain; THAT is the sniper experience as I know it.
Sniper encounters are supposed to be intense. The guy in the crosshairs is the underdog, and gameplay should reflect that. Remember the battle in MGS:Snake Eater with the old sniper, The End? Sniping should be like that: you're in sniper territory, the sniper's wearing camouflage and you can't see him, but you know he's here somewhere. He might even be watching you right now. He might be toying with you and waiting for the most demoralising moment to hit you right between the eyes, or else he might have got up, switched class and buggered off. You have no idea. The entire thing is a collossal mindfuck either way. Do you go further into sniperland and try to flush him out and kill him on your terms, or do you turn tail and go back to fighting the other classes? That's how I want to see snipers represented.