Trust in God, not in men.
The church is run by men, and men are fallible.
"It pains me to ask this, but my question to you is, how are you able to compartmentalize your faith with that which we believe to be true about freedom and all that freedom entails?"
There doesn't need to be any compartmentalization, you just need to recognize that you may choose not to partake in what you believe is immoral, and that it is also immoral to use violence to stop others from doing as they please so long as they aren't using physical force against others.
You choose to lead by example, and persuade people instead of using the violent force of government to alter their behavior.
The Non-Aggression Principle is very compatible with the teachings of Jesus.
I hope this helps, also you can always send Tom Woods an email about subjects concerning Christianity and libertarianism, he is very insightful.
Check out the Laissez-Faire Journal at LFJournal.com
"The State is a gang of thieves writ large." - Murray Rothbard