The only way to not credit an RBI is if, in the scorer's mind, the run only scored because the grounder was mishandled. A scorer would only rule that in particular instances--a one-hop smash right at a drawn-in second baseman, for example; a play where nearly anyone watching the game would agree that the runner at third would have been out at the plate.
However, since the middle infield was back, and shaded toward second base (double play depth), it is quite unreasonable to expect a second baseman fielding an ordinary groundball to throw home. He would either attempt a DP, get the force at second, or throw the batter out at first (if the ball was hit toward the RF hole, for example). You don't have to assume a DP, or assume that the team would attempt one. I see the 'irony' you're getting at, but you're taking it a step too far... all you assume is that the second baseman would have thrown to second or first, and you make that assumption based on where he was playing, and where the ball was hit. Nothing more, nothing less.