The ESPN article suggest that there maybe was a little more to it than money. The DA apparently was a source of headaches for the USSF, and they may have just decided to let the MLS and other big clubs run it.
Apparently, the MLS clubs in the DA weren't happy because the non-MLS clubs weren't good enough and they want to start playing more international teams. At least one non-MLS club wasn't happy because they got dropped down to a lower division even though they were competitive with or even better than the MLS clubs. Girls clubs were leaving the DA because they couldn't meet the DA's coaching license requirements, and the future of the girls DA was in doubt. One club's closest away game was 800 miles away.
On the other hand, maybe not making the World Cup caused a real revenue hit that's forcing some downsizing now. And with the women's national team's equal pay lawsuit, USSF is going to have to start paying the women more than they do currently. Maybe saving the $12 million really does make a difference.