Whatever the decision we ultimately settle on, the .308 hunting round is just too powerful for a tier 1 gun to have. Raiders in the CW need some kind of long-range weapon. If we merge all NV/FO3 weapons, then varmint rifle would work, but I think merging the weapon lists as part of the base mod is a bad idea. Short version: it's easier to scramble an egg than unscramble it.
I am still rabidly for keeping .32 as a caliber, despite the fact that it applies to only two weapons. It's lore-friendly, and really an iconic element of FO3. That aside, we should have something low powered in terms of a hunting weapon. .38 special could work, though we run the risk of oversaturating the .357-equivalent caliber weapons.
If we can't keep .32 as a caliber (seriously, can't stress enough how much I'd like to), I'd say we should pick a caliber that DOESN'T have a rifle weapon associated with it. For low level, right now that's either .22LR or .9mm. .22LR has the silenced .22 SMG, and for people running a specific mod the Varmint Rifle. 9mm on the other hand has no BASE rifle, although arguably since 9mm is taking the place of 10mm in the CW the Lever-Action Rifle should be chambered for it.
Anyway, that's my recommendation: stick with .32 as a caliber, and failing that go with a .22LR or 9mm rifle. What the weapon looks like beyond that... no idea.