Can we really reliably remove pitching from the equation? All the defense independent pitching stats I've seen assign HR allowed, BB, K, and HBP to the pitcher and everything else to the defense, which seems way over simplified. If this "discovery" is based on those assumptions, then I don't think it's worth all that much.
Fielding statistics have moved beyond this point - you should read a primer on UZR or John Dewan's work in The Fielding Bible, (or ask a SoSHer more knowledgeable than myself to give you a tutorial.) Basically, by looking at batted ball type (LD, GB, FB) and breaking the field down into zones used to track the location of batted balls, we can get a pretty good idea of how many plays fielders are making above or below average, and how many runs their efforts add to or take away from the team's RA total.
You're certainly correct, however, that until we reach a Hit F/X stage of stats (e.g. the ball traveled off the bat at angle x from the foul line, angle y from the horizontal, at velocity v) we may be crediting or penalizing certain fielders unfairly. There's also the issue of park effects, with Fenway's left field wall being the most notorious example. Ultimately, it wouldn't surprise me if as a result of the next wave of fielding stats, some of the runs currently credited to fielders end up being given back to other areas, either as credit to pitchers or as debit from the opposing team's hitters.
But the consensus right now seems to be that even if the best fielding statistics aren't perfect, they're pretty close, such that future deviations from the estimates they provide will probably be minor.
Everyone can agree that the game is 50% offense and 50% pitching and defense.
Actually, they don't need to be. As a wild example, let's say that advances in strength training mean that 20 years from now, every single position player hits like (what we now consider to be) a superstar, and that every team would score 1000 runs against an average pitching staff from 2009. Let's say that standards of pitching and defense also improve, but not in such a uniform manner, with the result that our future teams are normally distributed by RA tendencies - let's say that the average team allows 850 runs, while the best and worst allow 700 and 1000 respectively. Then you could, in a sense, say that the game is 100% pitching and defense, 0% offense, because a team's success or failure is entirely determined by how well they pitch and field.
Also, even if the talent levels are such that deviation in RS and RA comes equally from both sides of the ball, we can see from the pythagorean formula that a run prevented is slightly more valuable than a run scored (and pitching is more susceptible to being leveraged through bullpen use.) So even in that case, pitching/defense are slightly more than 50% of the game.