I think he'd be shocked about the moral decay of the country, the sanctioning of gay marriage, hostility towards Christianity, redistribution of wealth, massive government intrusions in the citizens freedoms ie.. Obamacare, the IRS, Social Security, Medicare, Gun control, an activist Supreme Court, the blatant disregard for the Constitution, the centralization and secularization of education and a host of other issues.
Jefferson wanted to prevent any Christian denomination from dominating the federal government but wanted to promote non sectarian Christianity and Christian values, as expressed in his actions as president. He regularly attended church services in the capital building with pastors paid by the federal government to preach on a rotating basis. He also arranged for Christian services at the war department of the executive branch. Federal funds were used to build christian schools and pay for missionaries to promote Christianity to the Indians.