Are you certain your memory of the 90's Cowboys is accurate. Honestly, up until a few years ago when I watched some of the games from that era, I thought the same thing - the 90's team was dominant in all aspects. But truth is, that really isn't the case at all. Memory can be tricky. You remember being wrapped up in the awesomeness of that team, but truth be told at many positions they had marginal talent with a few Super Stars on both sides of the ball.
So like the analogy above involving the clown fish and the anenome, that same relationship can be found across a team - a good defensive line helps pass defense, a good secondary can create sacks, a good linebacker crew helps both units respectively. Take a closer look at that 90's team roster, though. Sure, they had some excellent players, no doubt about that. But they also had fringe talent that benefited quite a bit from their surroundings. Furthermore, it is also important to note that the parity football enjoys today was not quite the same in the 90's. Every year it was pretty much the same teams in the running for the championship; now that landscape changes from one season to the next.
Now, don't get me wrong. I'm not suggesting that drafting Zeke will propell the Cowboys into the Super Bowl in 2016. In fact, I seriously doubt it for the same reason you are leaning towards drafting defense. But, I do believe draft Zeke will help the defense more than any other defensive player that is available.