President Obama's narrow victory among Catholic voters this week will be seen by many as a political loss for the U.S. Catholic bishops, who appeared to be openly opposing Obama during the presidential campaign.

The Catholic Church was well within its rights to conduct its campaign on religious liberty, but its "Preserve Religious Freedom" yard signs were clearly designed to be placed alongside partisan candidate signs. And they were - in very large numbers.

The technically nonpartisan nature of the Church's religious liberty campaign was further drowned out by a small chorus of strident bishops who left no doubt about how Catholics ought to vote for president.

In a letter he ordered read at all parishes last Sunday, Bishop Daniel Jenky of Peoria juxtaposed the Obama administration's new contraception mandate with the scourging and mockery of Jesus. Jenky declared that "electoral supporters" of pro-abortion rights politicians reject "Jesus as their lord," as did the crowd that roared, "We have no king but Caesar."

Such forceful statements were never balanced by significant challenges to the Republican presidential ticket.

There is more at stake here than politics.

Though I agree with the bishops that the exemption for religious employers in the White House contraceptive insurance mandate is too narrow, the bishops' posture toward the administration during the election poses a major risk to the Church because it left the impression that there was only one legitimate Catholic choice for president -- Mitt Romney.

The result is that half of the Catholic electorate felt it was being judged as voting "against the Church," even though such voters weren't actually dissenting from Catholic teaching. They were, instead, making the complex decisions that any serious voter must, weighing their own moral commitments against a candidate's professed values, the policies they propose and how much is likely to be accomplished on a given issue given the political climate.

Voters must weigh the mix of positions of both candidates, not just the objections against one. This year, they had to weigh, among other things, a new problem with religious liberty against the Republicans' earnest proposal to replace Medicare's guaranteed coverage with a subsidy for private insurance.

By putting voters in a "with us or against us" bind, some of America's bishops have risked eroding their own authority. They imply that specific political judgments are matters of Church teaching, when by Catholic tradition, the more they descend into the details of policy, the less certain their judgments become.

Bishops must allow room for and respect believers' own specific political judgments. The Second Vatican Council taught that it is primarily the responsibility of the laity to undertake the secular work of inscribing "the divine law...in the life of the earthly city."

The way out of this crisis is for the bishops to carefully respect the necessary limits involved in the task of forming the consciences of lay believers. They must teach moral principles and, yes, argue for their specific application, but always in a way that respects individual judgments about how best to enact these principles.

At times this formation might even require forceful challenge, but it should never assume ill will or ignorance when the faithful vote differently than they desire.

Trusting laypeople to make the political decisions that are properly theirs gives them room to embrace the Church's doctrines, even if they cannot enact all of them in their voting choices. This is essential to sustaining a Catholic identity separate from the divisiveness of partisan politics. This election season like none before left many Catholics feeling like the Church gave them no such room.

The Catholic Church will enhance its public authority by speaking out in a way that supports and challenges both parties. Prophets are respected when they are perceived to be an independent and fair voice. When the deep coherence of Catholic moral teaching is communicated, it can free people from our partisan moral straightjackets. But when parts of this teaching are passed over in silence, the Church puts itself in a partisan straightjacket.

The official Church response to the candidacy of vice presidential nominee Paul Ryan displayed this failure to forcefully challenge both parties. In the spring, the U.S. Conference of Catholic Bishops had challenged Ryan's proposed federal budget for failing to put "the needs of those who are hungry and homeless, without work or in poverty" first. But the bishops were largely silent on this issue during the campaign.

The response of Catholic voters, however, displayed a decidedly Catholic instinct for the common good. Introduced as a "faithful Catholic" by Romney, Ryan brought no significant bump in Catholic support for the ticket.

Indeed, Ryan's radical budget and ideologically driven plan to end Medicare as a guaranteed benefit program did what decades of work by Catholic social justice advocates had never been able to achieve: It activated a gut level Catholic concern for solidarity and the common good. President Obama's Catholic poll numbers peaked in the weeks following Ryan's selection.

The Catholic Church can never turn its back on the moral dimension of politics. But it must beware the divisiveness that even the appearance of partisanship can bring into the Church. Teach and preach the fullness of the Church's doctrines forthrightly and forcefully, but honor the decisions of the laity. The danger is not that the Church might inappropriately interfere with politics, but that partisan politics will infect the Church.

The opinions expressed in this commentary are solely those of Vincent Miller.