I don't think the Cowboys thought they would be in this situation they are in today. Nobody imagined at the time Dak would be the caliber QB he is right now, and were probably assuming they would have a ton of cap room by the time the Zeke Elliots contract was up in 2 years. They probably figured Romo had a few more years in him, and would go after a starting QB in the draft after a few years which would have a couple year gap between Zeke and the QB on the rookie scale.
They also weren't figuring that Byron Jones, Anthony Brown, Maliek Collins, and a bunch of players were not going to be guys who were going to exceed their draft grade.
Where they messed up is by trading for Cooper, because he puts a huge stranglehold on cap space, and IMO if Zeke doesn't take a deal the Cowboys feel is right he will be the odd-man-out considering how he has handled his career off the field, and not showing up to camp. The Cowboys have had his back, and he has turned his back on them, and yes you can argue the fact that they planned on using him up to get rid of him but IMO he is making that claim justifiable at this point.
If I'm the Cowboys I don't pay him Gurley money, draft his replacement next year and let him come back to the table when he realizes oh crap I can't ride this out 2 years straight of not playing and hit FA and expect to hit the jackpot in FA.
He either takes a lesser deal, or he walks, but if I'm the Cowboys I do not give Zeke what he wants based on his personality on and off the field. This allows you to sign your guys like Dak and Amari, and some of your other defensive players who are up for contracts in the next few years. The Cowboys are in great position they are going to add multiple 3rd round comp picks over the next few years to fill those holes if these players play as we expect them too.
Zeke isn't going to win this war, and he is putting himself deeper and deeper in the hole the longer this goes on.
