they're no better or worse or really any different than social clubs, book clubs, fraternities, or any of the other categories of non-profit organizations.
the problem is when such organizations engage in non-tax-exempt activities, most notably, politics.
responsible organizations separate their non-profit activities from their for-profit or otherwise non-tax-exempt activities. churches can (and plenty do) exactly this. thus a church can legally and legitimately engage in political activity within a non-tax-exempt organization, but continue to encourage charitable activities through a related non-profit organization.
so really it's a matter of enforcement. the law already provides the means to punish churches that engage in political activity, it's just that there doesn't seem to be great enforcement of this. then again, i don't know, perhaps the ones that do engage in fairly overt political activity have exactly the kind of legal separation noted above.
on the other hand, how much could the government really do to prevent people from getting together and taking political direction from someone they respect in their community? as tempting as it sounds to use the tax code as a weapon, i don't think much would change even if enforcement were to become very strict. churches could just separate their activities between non-profit and political, and keep the bulk of the money in the non-profit, enabling them to continue to engage in political activity while paying nominal taxes.
the only thing it might, *maybe*, accomplish is to make it a bit more difficult to mega-preachers to become filthy rich. i say *maybe* because there's no reason why the non-profit can't pay the preacher an enormous salary and bonus.