Well first off there is no separation of church and state with the issue of telling what a church can hire or not hire, this puts them into a labor issue and not a religious issue.
Second, the EEOC is following their guidelines and going after an entity which falls under the laws of the state of Michigan and the federal government with a number of things. They are not trying to say "you can't teach Catholicism to your students" or say anything of the sort, they are saying that the school failed to meet the requirements as an employer by allowing the person to have am medical leave of absence, then replacing that person with the reasoning that they do not have to accommodate her or follow the law.
Third the article is about the government's lack a proper case with the solicitor sounding like an idiot in front of the judges. The issue here is not whether the church has the right to hire who they want but they seem to think that they have a ministerial exception because they are running a school, which then can be used when they run a for profit business and tell the government to stick it when they go to collect the taxes.
So I don't see the "attack" as you claim, I see a need to define what the church can or can not do within the context of labor law. By the way, it has zero to do with Obama, this went on long before Obama was elected.
