Okay I'll lay things out as I see them and I'll try to take on criticism whether instructive or destructive because if you can think your way through adversity you'll find a position you can be proud of to support and help other find the position they need to support given their own morals.

*Assuming you read the article posted, here's how I want to start stuff out*.
First my flaws: Though I was raised in a Catholic (yes Christian) family, I am not the perfect son. Far from it, I've been a hypocrit many times throughout my life, I've done a lot of wrong. I'm still working on becoming a better person, and I may not ever be completely happy with how morally good I am, but my aim is to gain consistency in the morals I espouse along with how I act in everday life.
That being said...

I think the complicating philosphical matter is creating a distinction between what is morally prudent and what is practically/socially prudent and which sense of prudency to use in the political arena, whether voting or establishing a platform.

Inherently, Church-State seperatoin is a good thing given the history of the world. Take for example Medieval Catholic Italy or Early Protestant England. In both cultures people unfairly used religion for the sake of political gain and to coerce people based on "divine right". Putting power in the hands of the people is what modern society prides itself on because it prevents this immoral and unfounded use of religion for personal gain.

But what happens when a democratic political system is in place, one of secular basis, based on majority rule. The beauty of the democratic system of rule is that people are respected as individuals and it is in no one's place to dictate what morals a person has, so long as he/she does not harm their fellow man in doing so.

Fast forward a couple hundred years of social/political evolution...
You are in the position of being a voter for the office of president in a bipartisan political system. You are a pereson of religious background and one party supports your views and the other party supports the exact opposite.

The problem of the matter is, the other party that supports your oppositve view on the moral matter supports your views on a vast array of other things (make stuff up just so the argument works... to not change focus of the argument lets say this second party supports something that is easily agreed upon like human rights in general for law-abiding citizens). But the first party doesn't cover your views with respect to these other things as well as the second party does.

The problem is that because you are a man of faith and religious background, the one moral issue that the first party supports is recognized by your religion as the foundation of the entire faith.

Here's where the matter got complicated for me. The Republican party is pro-life but is in complete disagreement with a lof of my beliefs on social justice and even some of my partical notions of monetary policy and such.

Which do you give more precedent? Your religious morals or your practical intuition which you know would benefit a lot of other people?