The people defending him seem to be using the argument "First Amendment rights trump zoning laws". That basically every (Christian) person has the right to set up a church wherever and however they damn well please, and if the government tries to stop them by citing "zoning laws" or "fire hazards", they're infringing on their freedom of religion and therefore it's the government's job to pay for the church to be erected safely and legally.
So, damn, what a way to get free home renovations. First make a half-assed, unsafe addition to your house. When you get cited for it, claim the addition is a church and the government is infringing on your religion by citing you for it. Sue the government for the money for your renovation, and voila.
(though, reading that second article, this guy is apparently one of those "sovereign citizen" types who claims to be a citizen of Heaven rather than the US, so doesn't have to follow US law when it inconveniences him).