I think this is a mixed blessing for religious organizations. Many churches are in desperate need of ministers. This will not make it any easier for them to find people who are willing to choose a career path that offers very few legal protections. If religious occupations don't offer the same job security as secular occupations, then it is only natural that fewer people will undergo the training to become ministers.
I found it interesting that this court case didn't address the issue of breach of contract. However, it raises the question of whether this could also be a problem for religious employees seeking relief. If so, it would frustrate the plans of a religious organization that realises that it may be necessary to offer reasonable employment contracts to entice people to work for them as a career.
If the rights of a religious organisation to enter into contracts, that are enforceable by law, is tampered with, then it would be a severe limitation of its ability to function in the real world. On the other hand, if the courts are willing to fully enforce contracts made with religious organisations, then it could easily involve judicial involvement in internal religious affairs.