The rest of the article for context is interesting.
It seems that there is a compelling interest for a state's wildlife management to permit captive deer in order to set standards for captivity, record of origin, proliferation of the herd, etc. Management of the wild deer population is serious business, and chronic wasting disease is a real problem.
On the one hand, the guy was warned in 2003, sought a permit, was denied, and continued to keep the animals illegally until now. On the other hand, the warrant doesn't authorize euthanasia of the animals on site - only seizing and holding the animals until a further ruling of the court.
In other words, it looks like there was a reason for the state to intervene, but that due process was completely violated.
I had read the whole article as well, IDP. I need a better reason than "compelling interest" for the state to take a position at all on the issue. The State has assumed ownership of all deer for the purposes of "protecting" them -- for "the people", of course -- so in the course of making them "everybody's deer", they're now "nobody but the government's deer" and a private individual taking an "interest" without the government's permission is tantamount to poaching the King's game.
If you lived anywhere around here, you'd see for yourself that "management" of the wild deer population by the state is a joke; thanks to the environazis, hunting is so strictly regulated, we're literally overrun. Then we're treated to a scolding about how humans are "crowding the deer out of their habitat" and all such bullspit, when the fact is the deer's only natural predator around here -- people -- are not permitted to keep the population numbers reasonable.
If chronic wasting disease is the widespread problem as claimed, I see no evidence of it; the multiple large herds around here are the healthiest bunch of foliage despoilers you'd never want to see after your Azaleas. 
Furthermore, it is a well-known tactic by the government to claim a health issue/endangered species/crisis in order to acquire control, even if it requires manufacturing the evidence.
In conclusion, yes, the man broke the law, but did nothing wrong. The authorities broke their own law and DID do wrong.
In my opinion, there's no good reason for the law; it simply makes criminals of people doing no harm nor wrong.
That may be Pan. I know nothing of NC, so I based my comment on what I know about MN.
I know that here in MN, our deer population is strictly managed as a resource. We have problems with herds too close to cities and such too. But each fall we have around 1,000,000 hunters hit the woods. That's about 20% of Minnesotans. That number alone constitutes a "compelling state interest" - at least in my mind. The state manages deer as a resource for the public good and public interest as well as economic benefit to the state - both private business and state coffers. Part of that management is population control, quantity, and health. They count and estimate population; monitor disease, starvation, natural predation; and adjust harvest limits accordingly.
There are "deer farms" and petting zoos in various tourist locations. I don't know for sure, but my guess would be that they are regulated to ensure containment, veterinary records, and whatever other compliance must be met in order to ensure that the wild deer population is not affected by these businesses. I think that given the taxpayer resources that go into management of the wild population, regulating these businesses is logical and justified.
The one thing we DO have to worry about here that you don't in NC is winterkill. That may be the difference right there, in why we may need more invasive management here as compared to there. A particularly harsh winter with deep snow cover can kill an awful lot of deer.
But if I was going to make an assumption that the NC regulations exist for roughly the same reason they exist in MN, I would say that given the fact that the guy was warned in 2003 and continued to thwart the law (I keep thinking there must be SOME reason they didn't issue him a $50 permit), the state believed it was justified in intervening - but went off the rails in violating the guys due process by killing his animals without a warrant to do so.
I have to admit, there is a part of me that is curious as to the conditions these animals were living in, and the condition of their health at the time of the state intervention. Something's not adding up in my mind.
