Almost everything you just said was wrong.
Lets deal with noise first: The OP is planning on building a MAGE sniper. He will have access to the spirit concealment power. He will be firing on targets often from a significant distance. Noticing gunshots requires at least 1 hit on a perception test. Concealment + distance (or hell, just concealment alone) will be sufficient in nearly all circumstances. If not, there are other spells and powers that dampen sound.
A gauss rifle has a clip size of 10, and you are putting down one target per shot. These are not automatic weapons which consume ammunition at a voracious rate that we are comparing. The difference in clip size matters very little. A mass of targets will be deal with Stunball or a grenade launcher, not a sniper rifle or assault cannon.
Finally, the huge armor penetration of the gauss rifle will come up ALL THE BLOODY TIME. Do you not read anything UmaroVI posts? If are a mage, then you are using your weapon to do what your spells cannot - to shoot through walls, or to kill someone in a vehicle. Also, I've heard there are these things called spirits. I'm not sure if they are in this edition of SR, but if they are, I'll bet all that Armor Pen will come in really handy somehow.
Oh, I know, how about cyberlimb-armored orcs or trolls? They can easily have more armor than a vehicle. Or do cyberlimbs not appear in your games either? No spirits, no walls, no vehicles, no cyberlimbs? That's weird, man.
So I'll bottom line it: If you are using you are making good use of your abilities and playing intelligently, a gauss rifle is hands-down superior. And it's MORE superior the tougher your opposition gets.