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Health care reform is a long way from completion (leaving aside here the important question of the extent to which the House or Senate bills will bring actual "reform" instead of mainly "more of the same").  So it is too soon to judge the consequences of the changes for religious institutions and individuals--but not too soon to be worried.
 
1.  Abortion.  The House bill has robust language (the "Stupak amendment") to keep the federal government from supporting elective abortions.  The Senate bill's language is weak and troubling. 
 
2.  Conscience protections.  The House bill includes a section (259) to protect medical staff and institutions from being penalized by government for not offering, referring for, or paying for abortions.  The Senate bill does not include this provision. 
 
3.  Diversity requirements.  The Senate bill includes funding for mental and behavioral health education and training grants.  To be eligible, an institution must show a "knowledge and understanding of the concerns" of "individuals and groups from different racial, ethnic, cultural, geographic, religious, linguistic, and class backgrounds, and different genders and sexual orientations."  In addition, the institution must show that such diverse individuals "participate" in the institution's programs (HR 3590, sec. 5306).  Empathy with and understanding of patients is of course important--though a professional does not need to be of the same group as a patient in order to be empathetic and to provide excellent help. 
 
But does this language (such diversity must be reflected in the institution itself) mean that an institution of a particular religion or that for religious reasons maintains traditional sexual standards would be ineligible for these education and training grants?  What makes this a relevant and acceptable condition of eligibility?
 
(The US Commission on Civil Rights has issued a letter about the House bill and another one about the Senate bill, pointing to a number of unconstitutional affirmative action requirments. Hat tip to Hans von Spakovsky.)
 
Given the significant divergence today between various secular standards and the deep convictions of many religious institutions and individuals, it is no doubt difficult to implement sweeping government regulations and programs while manifesting respect for those convictions.  This is all the more reason why, if institutional religious freedom is to exist, policymakers need to design their rules and programs from the start with a deep commitment to preserving that freedom.  A freedom that is protected only because a legislator or two managed at the last minute to wrench a concession from the majority is hardly on firm ground.

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The Pew Forum on Religion & Public Life recently released a new international study, Global Restrictions on Religion.  The careful study considers both governmental policies concerning religion and religious institutions, and private actions that respect or curtail (e.g., mob violence) religious freedom.  The report merits careful reading, given how important religious convictions, actions, and institutions continue to be in every society.
 
Unfortunately, as detailed as the report is, it does not provide sufficient information on key topics.  For example, in recording the proportion of countries in which the government provides funding or other support to religious groups and religious education, the study rightly distinguishes not only between those that offer no support and those that do, but further divides those that do provide support between governments that provide the support on an equal basis and those that discriminate when supporting religion. 
 
But what kinds of support policies constitute fair distribution and which reflect an unjust bias?  And does fairness require treating on the same basis not only the various religious organizations and communities, but also the non-religious groups?  Moreover, if a country supports only secular groups and institutions, but no religious ones, isn't that policy by itself already a policy of unequal treatment based on conviction and belief?  The report doesn't tell us.
 
As the report itself indicates, actual religious freedom is comprised of such details and not simple governmental assertions of a commitment to religious freedom.