In all fairness, Jimmy Johnson coveted James Francis, a LB out of Baylor. Johnson spent a good deal of time during the first round on the phone with Kansas City, trying to swing a trade for the #13 spot, with the intent of drafting Francis. The Bengals screwed that plan by taking Francis at #12. Even after that, Johnson tried to acquire Francis from Cincinnati via trade, but the Bengals wanted nothing to do with it. Then and only then did he set his sights on Emmitt, and worked the trade with the Vikings, giving up his 1st rounder (#21), and 3rd rounder (#81).
Of course, had Johnson understood the rules governing the supplemental draft, (he didn't know drafting Steve Walsh would cost him what would be the #1 overall pick in the 1990 draft), there's a good chance he wouldn't have drafted Emmitt after all. Had he not drafted Steve Walsh, he would have most likely taken either Cortez Kennedy or RB Blair Thomas at the #1 spot. Don't get me wrong, Jimmy Johnson is one of the smartest football coaches I've ever seen,. This was one time, however, when ignorance on his part benefited the Cowboys.
I understand the OP's point of trading a 3rd-wounder, but I don't see this as the same type of situation at all. There were TWELVE running backs taken in the first two rounds of the 1990 draft, including some guys taken after Smith who turned out to be pretty good (Rodney Hampton was probably the best of the rest, but Reggie Cobb and Dexter Carter also ended up doing well in their careers). Had Dallas not traded up with Pittsburgh, they still would have had a good lot of RBs to choose from at #21. That wasn't the case this year with Demarcus Lawrence. There was nobody that Dallas valued as a capable weak side DE after Lawrence. In my opinion, that made the idea of trading that 3rd wounder somewhat understandable.
There was no outrage that I recall when Jimmy Johnson did it to take Emmitt. Had there been, however, I believe it would have been justified, simply because there were still some very good RBs available after Emmitt was gone.