Huh? If you'll notice, the fire modes are entirely different.
The main fire has much less of a delay between shots, you can run around whilst shooting, but it does less damage..and uses less ammo.
Activating the sniper mode ( alt-fire ), you get a much greater time between shots ( so you have to be more strategic about using it ), it uses more ammo, it does more damage, but you can only crouch walk around...no running. You also get the satisfaction of disintegrating them if you charge the weapon fully.
So, it's basically like any other weapon. There is a main fire and an alt-fire, and they just behave differently.