I don't think there's a need to recognize any church or organization in general by government. We need to avoid letting any organization, be it religious, scientific, or political, have major influence in government decision-making.
The solution I would like is for all to be able to voice their religious, political, and scientific opinions in the sphere of politics and government regardless so long as these don't call for silencing inalienable liberties like right to life, right to vote, or right to free speech of other demographics.
We should simply put issues like abortion or homosexuality or evolution to a vote and let the people decide. There's no need to distinguish this group or that group. Just let it be an up-or-down majority vote. Let all people voice their opinions on the issues and trust the most persuasive, reasonable arguments will be adopted by the majority, simple as that.
While an organization can usurp government as a dictatorship, because it involves power in the hands of a few, it is far more difficult to do so with a direct democracy where organizations are not given this power but all may vote on an issue. What I'd like to see is the top political issues put on the ballot and have people vote on how to decide them each election. Same with a few of the top bills. The system would be tough to set up but could definitely be done if people can vote constantly on something as trivial as American Idol.
We shouldn't be upholding organizations through government at all. But we are of necessity going to have to adopt the VIEWS of organizations. Either Pro-Life or Pro-Choice will be the law, e.g. Or at least somewhere on the scale which will probably be supported by one side and not the other. In other words, we can have the issues of Evolution or Abortion or Marriage voted on by the people without instituting a specific organization in law, because organizations have nothing to do with this, but rather the will of the people themselves.