The agreement Senator Susan Collins claims to be engineering to consider modifications to the Gay Marriage bill will almost surely put the matter in Clarence Thomas's lap at SCOTUS in a matter of months. That is why opponents are so ready to reconsider.
Suggested changes to the language sound innocent enough; grant people with strong moral convictions the latitude to not participate in officiating gay marriages. Thus, officials like county clerks, justices of the peace, etc. have the option of opting out of performing gay marriages. Therein is the loophole.
Not so long ago, country clerks refused to marry gays on just such grounds. They generally got away with it. Now imagine if city, county, and state officials decided to not recognize gay marriages based upon the same religious grounds even if a gay couple found an official to perform their marriage. Inheritance rights might be abridged, joint ownerships, joint tax filing, citizenship applications, and the many other rights of married people. In some places, even today, you cannot get a wedding cake for a gay wedding reception on religious grounds.
Subtle language modifications have huge potential to undermine the entire aim of the bill - to make marriages between two consenting adults immune from SCOTUS personal biases. Those changes will surely risk triggering court appeals that will give Clarence his shot at declaring gay marriage illegal, or like abortion, make it nearly impossible.