As a veteran marksman who served 4 years in Afganistan I'll just weigh in on one thing here.
Yes, clearing rooms with a sniper rifle is unlikely to be very effective, but if you're the team sniper you shouldn't be doing that anyway. During CQB maneuvers the sniper and spotter more often than not provides overwatch for the rest of the team, covering exits and making sure the team isn't surprised y serving in an information gathering role and force multiplier as usual.
I carried a pistol as my sidearm during my service, and I never once fired it in combat. I also didn't clear houses on a regular basis. That being said, I have run breach and clear simulations with both my rifle (a Sako TRG-42 with a 28 inch barrel) and my pistol (an H&K .45 USP Expert). My experience is that it's perfectly possible to sight down the barrel (having first detached the scope, primarily so as not to damage it) of the rifle similar to how one would when shooting clay pidgeons with a shotgun.
Is it practical? No, not entirely. Is it impossible? Not at all. Do I think a system like Shadowrun, the combat rules of which are already massively abstracted, needs penalties for using traditionally "long" weapons in CQB operations? No.
Personal opinion only; if you're going for realism in Shadowrun you're going to have to change a whole lot of things, and this is something that would be pretty far down the list in my opinion.
And for those of you who've never fired a gun in real life, the good news is that TrackingPoint has you covered. Now you can be an expert marksman for just 30,000USD. :-)