UPDATE: Here is the text of the amendment, offered by Sen. Brownback and adopted by the Senate, intended to protect First Amendment rights:
Nothing in this division, or an amendment made by this division, shall be construed or applied in a manner that infringes on any rights under the first amendment to the Constitution of the United States, or substantially burdens any exercise of religion (regardless of whether compelled by, or central to, a system of religious belief), speech, expression, association, if such exercise of religion, speech, expression, or association was not intended to--Section 10 of the Hate Crimes Prevention Act also contains other provisions on construction of the Act and free expression.
(1) plan or prepare for an act of physical violence; or
(2) incite an imminent act of physical violence against another.