I don't think concern for it should be dismissed in the push for marriage equality, although I do believe that most of the fears are overblown. But the Connecticut law seems to me to strike a very good balance:
Religious groups warned that the bill would infringe on religious freedom and did win a late bipartisan compromise, as sponsors agreed to modify the proposal to more explicitly exempt church-affiliated groups from some provisions. The language closely mirrors that in a bill recently passed in Vermont, overriding a gubernatorial veto to legalize same-sex marriage in that state. The language expressly permits churches and related organizations - including church-owned venues and adoption agencies - to continue to discriminate on the basis of sexual orientation as long as the specific services that discriminate do not receive funding from the state or federal government.