So churches should be taxed because they use effective organisational structures and are well run? That’s a new one. You could say the same of well run charities.
If you think Christianity is broadly good and correct, the trend towards business-like megachurches and celebrity pastors is deeply corrosive to the faith.
If you think Christianity is broadly bad and corrupt, the trend towards business-like megachurches and celebrity pastors entrenches and effectively promulgates many of the religious ideas that you abhor.
If we're fair to what it is being said, the point seems to be this: churches are like corporations: their goal is to grow in size and revenue.
That is demonstrated by the anecdata of a friend, someone high enough in a particular church, that confirms they only spent 10% of their income on charity.
So the gist seems to be this: if it looks like a duck, swims like a duck, and quacks like duck, it must be taxed like a duck.
Not a bad argument per se. However, it lacks supporting data, preaching for those who already feel that religious institutions are a scam anyway. So, because of that, it's not very persuasive.