>there is no way anyone could decide whether it was a "net benefit" to society,
That's a viewpoint problem in itself. Liberties and individual rights should never be added because they are a 'net benefit'. I see the converse as being true, liberties and individual rights should only be removed if they are a significant detriment to society. In your example of gay marriage there is no data that it is harmful, therefore no reason to prohibit such actions.
Of course proving something is harmful is not a carte blanche to prohibit most actions. For example our 'war on drugs' motivated as doing good against the evils of drugs as turned into a rather harmful system in itself. Other systems that treat drug users rather than punishing them have much better outcomes.
So, from whence comes individual rights? The usual argument is, "imagine if that were you!"--that's empathy. More seriously, we guarantee individual rights for others because that means we have them for ourselves.
This leads to my second point: I think the reason empathy even is a thing is that we are inherently selfish, and for anything to be really done for the "greater good" individuals need to either have a stake in that greater good or they need to trick their selfish selves into thinking they are actually in that situation too, which, again is empathy.
Empathy works for the most part. It sounds like the author is trying to fix something that isn't broken. I'd say the current problems in Washington are in fact a lack of both listening to data _and_ a lack of empathy. I think more empathy would be beneficial, not detrimental.