The problem for the Warriors thus far is OKC's small line-up.
Durant/Ibaka is a long, athletic frontcourt that is capable of handling switches effectively it seems, and is still pretty intimidating at the rim. Considering the Warriors infamous small line-up... while it's lethal as well, it's still relatively small as far as.. shot blocking goes on the other end.
So, what the Thunder have been able to do is space out the Warriors. There are times when Green, the tallest guy on the court, is nowhere in the paint because Durant/Ibaka can shoot threes which makes paint points a cinch. This is actually the Warrior's Achilles heel that hasn't been taken advantage of that much until now. Westbrook/Durant on the run is nearly impossible if everybody is just the same forward height.
Then on the other end, switching with the Warriors and forcing them to play OKC's game of isoball just isn't going to cut it with that length. Adams/Kanter get taken advantage of but once it's Durant/Ibaka, long quick shots are actually what OKC wants. Everybody on OKC seems like they can guard their match-ups one-on-one with this line-up no matter what guy is on any of the five guys. Whether it's Curry on Ibaka or Green on Waiters.
The free-throw disparity is another thing but the Warriors are ranked 23rd overall. When you just shoot jumpers... that's kinda what happens though.
tl;dr Thunder so far have been more dangerous small than Warriors going small.