Well, the SC opinion was written at the time about banks, it just holds true about most everything. That why 'sin taxes' are set so high, its a way of discouraging people from buying those things. Given the property that a lot of churches have, even a property tax might well prove deadly (what's the value of a cathedral? The land it's on?), and that's a tax before I take 25% of their donations and contributions. Hey, Render unto Caesar and all.
But, we do have some laws in this regard, and it would be nice to see them enforced with respect to outright political activities - which would at least limit the outright use for Republican campaigning. Several court cases have found that the political restrictions on religious/not-for-profit groups does NOT extend though to things like ballot issues (gay marriage) which is not a strictly political or partisan deal.
What little enforcement there is of the laws however does prevent them from going whole hog, and I'm not sure that the very churches you dislike the most - the megachurches/the RCC/the LDS which are rich enough to pay taxes would not go out and form their own PACs (which they could then do, and that money is tax-free) and flat out endorse candidates with massive public ad campaigns. And, to be sure the RCC/LDS are very sophisticated at modern uses of propaganda and advertising and would prove to be a very powerful opposition. Hell, they are hard to beat now, just imagine if they could do more.
What we need to do, and have had a hard time doing (at least the TG community - and I use that word loosely - as opposed to the L/G community) is getting an equal number of people out there to publicly counter the church groups.
Which is why so many L/G persons have no trouble as some would say, throwing the T faction under the bus, because really, its not offending anyone who is really there. While the gay movement had to get out, get in people's faces, do that 'We're here, we're queer' thing, had to get all sorts of people to 'come out' (watch Milk, and one of the first things he does when the Brigg's campaign starts is to tell everyone at the meeting they have to come out publicly - they have to BE OUT for this to work) the TG community seems perfectly at home with the notion that it's best and brightest can in essence hide under the notion of stealth and someone else can go out and do the heavy lifting.
It's very hard to sell anything politically if one side is all big, public and obnoxious and the other side isn't even there.