The headlines are misleading. At first glance, it reads like the Church is using their charities as political leverage to advance their political agenda, seemingly flying in the face of a mission that should be more important than politics. If you read the article, it turns out that, from the Church's point of view, they have no choice. The anti-discrimination portion of the law would require them to recognize the gay marriages, which is very much not OK for the Church. So if they want to continue the charities, they are left with two options:

1. Break the law by not recognizing the marriages of any gay employees, and therefore land the church in legal trouble.

2. Recognize marriages that their religious views are incompatible with.

Neither one of those choices are acceptable to them in any way, so their only choice under the current wording of the law is to cancel the programs. And as much as I despise the Catholic Church, I can hardly blame them for this logic. And I'm sure it's a very hard choice for the church leadership to have to make.