The team obviously wasn't in salary cap hell, but they were absolutely cap constrained. Cap hell is having like 1/3 of your cap in dead money a la Oakland.
However, they certainly couldn't have "done whatever they want" this year. They had just about exhausted every possible restructuring option available to them. They could have squeezed out a few more bucks with a long term Spencer extension, but that is going to cause issues down the road and they had the Free restructure/pay cut left. That was about it.
So, they are a little under now. They can extend someone or roll it over to next year as a credit. Unfortunately, they have about $140 million committed for next year on a flat cap.
http://overthecap.com/teamcap.php?Team=Cowboys&Year=2014
That is a new site I haven't used much, but we can use it for argument's sake. Not a lot of dead money in 2014 (which is how I'd define cap hell). However, they need to cut $20 million off before next year. Lee, Hatcher and Spencer are free agents, I think. Dez in 2015
There are a few guys you can restructure for significant savings (Romo, Ware), but you again increase the cap hit down the road. A few guys you can cut (Rat, Livings, Bernie), but no real depth behind them.
So, my opinion, not cap hell, but not exactly a good cap situation nor a situation where you can go do whatever you want in FA. Teams do get in this position, but they are usually Super Bowl caliber teams trying to keep a core together for a final run. Dallas is an 8-8/non-playoff team trying to do that.