Honestly, it depends on the type of game that you want to have.
In a game that focuses on deathmatches where everyone has to hold their own, you really can't just let everyone hunker down with sniper rifles in different corners of the map or else the game will get incredibly boring, so no, you can't allow ohk's for body shots (regardless of whether it makes sense or not). From a gameplay standpoint, it simply isn't allowable, so reality has to get bent a bit.
If you're trying to emphasize teamwork in a larger, more strategic combat scenario (one with actual objectives other than, say, "kill the guys in blue"), there are a number of things that you can do to both balance sniping, and allow for OHK body shots.
1. Force the sniper to deploy for any sort of ranged accuracy. This means either nuzzling up against cover (like a wall) or going prone, resting their weapon on something to steady it. This process should take a moment or two as the sniper gets situated, deploys their bipod, etc, and also limit their field of view somewhat, so they're overlooking an area rather than being able to spin like a turret.
2. Again, since this game is (apparently) focusing on teamwork, the appropriate way to counter a sniper would be to guesstimate where they are, then either send someone around to flank them while they're absorbed in sniping, or have a support class fire a LAW or similar long-range explosive to either spook them into redeploying (buying time) or eliminate them outright. The advantage of a sniper should be that they're extremely lethal at long range, but very vulnerable up close.
3. Give the sniper a reason not to fire. If providing intel on the opposing team is setting up can be just as valuable as attempting to actually engage, you let snipers fill into their true niche - intel gathering, with the ability to harass (not usually outright eliminate) oncoming forces, and support advancing forces. Give them the ability to place temporary virtual markers only visible to team members (with a few preset icon for things like 'supplies here' and 'enemy position'), sight laser designators to allow nearby ally command-classes to call in drone strikes without manually targeting, and a limited ability to track enemy heat signatures behind cover (but being unable to fire in this mode), and you have a class that is almost as valuable when they stay hidden as they would be when actively engaging an opponent.
[edit] With a bit more thought, only upper torso should be a OHK. Limb and lower torso (gut) shots should partially disable a player, killing them after a countdown (lets say, 20 seconds) unless a medic class can get to them and stabilize them. Aside from being a bit more realistic this also allows the sniper to set up the classic situation of one person being wounded and bleeding out in an open killzone while his buddies desperately search for ideas.