I am sure you will be able to do that. While I disagree with you about monsters having to be built with the same system the PCs are, I do agree that the system should be as flexible as possible.
I don't care if PCs and NPCs use the same system. It's the end result that matters. If NPC goliaths wield big freakin' weapons because they're somewhat oversized, then PC goliaths should be able to, as well. If it's unbalanced for PCs, just say it's not a PC-able race -- isn't that pretty much what you'd say about a pit fiend? The only difference is scale.
I'll make the concession that it could be the "big" racial ability or that it could even require a feat (or feat tree) to do, but a PC needs the potential.
One of the things I hated about oD&D was the long tradition of having NPCs (usually wizards) who could do some interesting things or make neat toys that the PCs never could. "Because he's an NPC" is an absolutely horrid reason for an ability. Make it require 40 years of study or the bartering away of one's soul or something else prohibitive, just don't make it truly impossible.
With the over-sized weapons, I'm just afraid that there is no good excuse, though. It's inherent to the race, for NPCs.
I'm not saying that the PCs and NPCs need the same builds or stats. But saying that PC goliaths cannot use oversized weapons is as ridiculous as saying PC wizards can't cast fire spells. Sure, an NPC wizard may have a rechargeable fire spell, while the PC doesn't, but they can both do it. Maybe the goliath gets a racial daily stance that lets him wield oversized weapons for the duration of the encounter -- it tires him out, but he can do it when the chips are down.