This whole thing is blown out of proportion. CfA has been an outspoken advocate of Christian values since the company was founded, so it's not like this is some great new revelation that they believe in the traditional definition of marriage. The CEO was asked, by a Baptist publication for that matter, for a comment on marriage and he gave his opinion. Someone ran with it in the media and created an issue out of something that was already known to most people.
Personally, I don't believe homosexual couples should receive any different treatment than heterosexual couples. I believe the definition of marriage should still be "man and woman", but I believe that any tax break or incentive to be "married" should be available to either couple.
However, the thought that public officials in Boston, Philadelphia, and Chicago have stated they will block any attempt for CfA to start a business within their cities screams of religious discrimination, which is exactly what all of the "right wing redneck nutjobs" are upset about.
So religious groups should be free to push for discriminatory legislation? Their right to religious freedom gives them the right to force that religion through legislation?
Personally, I don't think the government should be involved in marriage at all. As far as the government and benefits are concerned, everything should be a civil union.