If the delay truly was ATC, then yes, that is traditionally extraordinary circumstances and not subject to payment. But this could also be a convenient response from Delta to avoid paying out the penalty.

Did any Delta employees at the airport describe the reason for the delay in detail? If so, what did they claim was the reason? Any details are important here...

If you have doubts about whether ATC was the real cause of the delay and would like to escalate to a third party, I recommend writing a letter to the AESA, the Spanish regulatory authority. In my case for an ex-BCN flight, they were very helpful requesting information from Delta and making a determination on whether compensation was payable, which resulted in the full value of my claim being paid by DL.