The thing you guys have to consider is that the basic Sniper Rifle has a comfortable zoom that allows you to strafe while charging a shot that will variably insta-gib with preference to shooting the head. This is the defining feature of the class, much in the same way that the defining feature of the scout was to be annoying.
Also in the subtle way that the medic's actual primary, the heal-gun, was given a dynamic partner in the Kritzkrieg. The Blutsager was just a blatant upgrade to the needlegun, same with the Ubersaw.
I like the idea of a Boomerang for melee alternative so far. It maintains the cherished ideals of the kukri: a weapon of desperation for the sniper caught with his pants down, or a trusted companion for the experienced and daring.
So with that in mind, I was thinking of something for the sniper rifle to radically alter it's playstyle, yet still suit being the god damn Sniper instead of some sort of Soldier Jr cadet or hallway camping kamikaze. The Soldier and Pyro already do those things!
My first idea was a rifle that disables head shots/crits, does a clip more decent damage(current base is 60ish, bump it to 80ish) and does X Interesting effect. I suggested a bleed effect. A one-time, Natasha and 1/2 slow would work. For cosmetics, the thing leaves a trail as they bleed. This is because whenever I play Sniper, I like to sneak up on Heavies and loudly announce that I HAVE CAUGHT A WHALE YAAARRRR. And the name writes itself: Blood In The Water. Give it a cute little jagged shark motif and BAM. This rifle suits Snipers like myself who prefer to act as suppressive fire, taking the headshots WHEN WE CAN, but content to simply body shot a soldier twice with whatever charge we have and let him go find a health pack.
For a more practical idea, especially as far as altering existing paly styles go, I'm thinking of a REALLY FANCY high-tech(as far as the art style allows) tri-pod rifle that lets the Sniper do something drastic, like change his "silhouette." If you didn't know, every class in TF2 is designed to cast a distinctive silhouette that lets you recognize them immediately. It's also pretty key to sniper on sniper fights or recognizing the danger of a sniper.
Anyway, it's a fancy tri-pod rifle. Maybe it has a taunt/sandvich/bonk style animation that lets you lie down. Maybe it can shoot around a corner JUST A LITTLE, only your extended rifle scope revealing you. Or a comical lens flare. The sniper is wearing shades: he'd dig that sort of cheesy coolness.
I dunno what else it might do.. maybe it has a bit of automatic fire or variable zooms or better damage, but I like the idea that for the top dog sniper or the highly compact team, pissing away five seconds and leaving yourself wide open to revenge from the rear is worth a shift in play that'll let you wreck havoc across a chokepoint or a charge. Granted the more I think about it, the more I realize this is the sort of esoteric thing you might replace the SMG with.. the Sniper Rifle really needs to be intuitive.
But hey, whatever Valve does, as long we don't get more blatant upgrades like the Ubersaw or KGB. The Pyro update had the perfect meshing of practical, varied and refined subtlety...