As David pointed out, it's ok for a church to commit capitalism as long as the profit it makes is used for doing charitable things, like feeding the poor or repairing the church roof, for example. I'd think there would be limits, like for example could a church make millions of dollars in profit and then decide to pay its pastor those millions of dollars? Seems like Jeremiah Wright gets a pretty good paycheck though, so who knows. Maybe I should designate my house as a church.
When it comes to a church, or any charitable organization, using leverage its investment has to bully a business it's invested in into following church doctrine, that doesn't seem right to me. But I'm not a lawyer. Maybe we could ask Lois Lerner; I think that's her department, or was, and she should have plenty of time on her hands these days.
A church that follows liberal doctrine on civilian disarmament should read the Bible more closely. This is something Jesus said on the subject when he was getting his disciples ready to go out on the road without him:
And He said to them, “But now, whoever has a money belt is to take it along, likewise also a bag, and whoever has no sword is to sell his coat and buy one." Luke 22:36