Like the ADA, once everything shook out, fewer disabled people were hired because employers didnt want the hassle.
The same will hold true here. Any indication of an interviewee in a same-sex marriage will result in that person not being hired. That, or many of these charities will simply stop taking federal money, which will hurt charitable outreach. Catholic Charities is the largest charity in the US and its influence is extensive. The government, by itself, can't duplicate it.