Auto aim in sniper mode is an awful idea. In fact, it's generally awful in all circumstances except high speed close range battles (i.e. swirling medium tanks). At long range, autoaim will still lock on to the middle of the hull, even if that part is behind cover. So if you're up against a hull down tank and trying to snipe you will miss almost every shot. The sensitivity of your mouse can be set independently for normal and zoomed mode. Crank the sensitivity down on zoomed mode.
Many higher tiered tanks have invulnerable sections and weak points. If you want to hang at T7 or higher you will need to aim every shot. Personally, I hardly ever take a shot without zooming in and aiming at a particular point on the tank. For example, against a Tiger 2 you must shoot the lower glacis, against the IS4 you must shoot the driver's hatch, against a KV-5 you must shoot the radioman's turret and against a Tiger P you must shoot the turret.
Even when your aiming circle is as large as your target (i.e. at long ranges), the circle is center weighted. Therefore, you're more likely to hit in the middle than at the edges. It is critical to aim your shots at long range. Even if it seems like half the circle is off the target by aiming at the lower hull or turret when sniping, if that is the area you can penetrate, the center of your reticle needs to be on the weak spot. I would suggest weening yourself off autoaim immediately. The sooner you can get rid of it, the sooner you can go up a level in game play.