Churches don't pay taxes, but instead they add value directly back to culture, through charities, as one example. How many hospitals are named after Saints? Way before it was fashionable, the Churches were helping with medical care.
That was then. This is now.
https://rewire.news/article/2014/06/24/dispelling-six-myths-catholic-hospital-care-united-states/
"Over the past decade, Catholic hospitals have merged with and purchased nonsectarian hospitals around the United States, becoming leading players in the nation’s health-care industry.
Catholic hospitals receive billions of taxpayer dollars each year and have a combined gross patient revenue of $213.7 billion."
http://www.washingtontimes.com/news/2015/sep/24/catholic-church-collects-16-billion-in-us-contract/
"The Church and related
Catholic charities and schools have collected more than $1.6 billion since 2012 in U.S. contracts and grants in a far-reaching relationship that spans from school lunches for grammar school students to contracts across the globe to care for the poor and needy at the expense of Uncle Sam, a Washington Times review of federal spending records shows."
What they add to the culture seems to consist of whining that they can't put humungous crosses on the city hall lawn, or impose their prayers on school-children.
Instead of needing an expensive social worker and therapists, like today, the priest, rabbi or pastor, did it for free. This lowers social costs.
That depends on how you tot up the social cost. The guy who makes confession on Sunday will beat his wife again next Friday night; the gay youth who turns to his rabbi is told to shut up, get married and make little Jews; the terminal cancer patient is visited by a minister who tells him that if he tries to escape another three months of suffering, a loving God will make him suffer for eternity. And lots of little children are afraid to fall asleep.
Consider a scenario, where instead of paying taxes, you have the option of providing an equal value of goods and services, to the community.
Who keeps the books? Where is the = ?
Such an arrangement as you suggest could work very well - under a competent secular government.
It cannot work with institutions that
1. provide services patchily, by district and population
2. choose the services they're willing to provide and refuse other kinds
3. discriminate among the people they're willing to serve,
4. each have an internal hierarchy with its own value system
and 4. tolerate no oversight or quality control