Justice Stevens was not inconsistent in his interpretation of the Constitution's religion clauses.

J. Brent Walker writes (in WaPo):

Justice Stevens has been a friend of church-state separation. His Establishment Clause jurisprudence has always been strong. He has uniformly stood against government-sponsored religious speech and endorsement of religion. He has been just as critical of attempts on the part of government to fund religious organizations and activities.

However, his willingness to require (or sometimes even to permit) the accommodation of religion under the First Amendment's Free Exercise Clause has been lacking. He joined the Court's conservatives in Employment Division v. Smith, the Native American peyote case, which gutted the Free Exercise Clause of its robust religious liberty protection for all Americans, not just Native Americans. 

"However" is the wrong transition. "Accordingly" or "by the same token" would be appropriate. A strong position on the separation of church and state, at its most consistent, leads to the idea that neutral, generally applicable laws do not violate the the Free Exercise Clause. Smith validated uniform laws as they are applied to everyone, with no exceptions required.

Here's Justice Stevens, in a concurring opinion, in Boerne v. Flores, in a case in which a church in an historic district wanted to enlarge its building:

If the historic landmark on the hill in Boerne happened to be a museum or an art gallery owned by an atheist, it would not be eligible for an exemption from the city ordinances that forbid an enlargement of the structure. Because the landmark is owned by the Catholic Church, it is claimed that [the Religious Freedom Restoration Act] gives its owner a federal statutory entitlement to an exemption from a generally applicable, neutral civil law. Whether the Church would actually prevail under the statute or not, the statute has provided the Church with a legal weapon that no atheist or agnostic can obtain. This governmental preference for religion, as opposed to irreligion, is forbidden by the First Amendment.

The Religious Freedom Restoration Act, Congress's response to Smith, was an attempt to create by statute what the Court had rejected as a constitutional requirement: exemptions from neutral, generally applicable laws that burden religion. Stevens, alone of all the Justices, thought that RFRA violated the Establishment Clause.

Do you think government should be able to give religious persons and groups "a legal weapon that no atheist or agnostic can obtain"? Do you think it's conservative or liberal to say no, as Justice Stevens did?

Walker dings Stevens for "join[ing]  the Court's conservatives" in Smith, but Justice White was also on that side, and Justice O'Connor was on the other side.  Walker seems to think that he's bolstering his position on the Free Exercise Clause by associating it with conservatives, and it probably is safe to assume most Washington Post readers think like that. But with the religion clauses, it's not so easy. If you're a liberal who cares deeply about the separation of church and state, why would you favor religion-based exceptions to laws that otherwise apply uniformly?