Cause why would he be able to just control the spirits? A skill which obviously nobody else has the faintest idea how to preform and yet he was able to preform it on a mass scale perfectly.
Also why wouldn't he teach that skill to Korra at any point on their trip? She probably could have done it if she was trained rather than just aping what she had seen work. He didn't tell her probably because it would have exposed his secret.
Maybe because it takes a while to master? You don't just learn some particular bending technique overnight. Especially Korra, who by all accounts is like one of the least spiritually inclined avatars that we've ever seen. (Although she managed impressively nonetheless, what with her managing to make the spirit stop for a moment even if it didn't last)
Bending has always been confirmed to be part genetics, part spirituality. That is why the old Air Nomad population were
all benders. And since the statue that Jinora saw at the end had the same kind of swirl-pattern around it, there's no need to assume that Unalaq is the only person ever to have been capable of doing so, just the first person we've
seen doing it because we've never had experienced, spiritually inclined benders deal with angry spirits in the physical world before. The only examples of those are Hei Bai and Wan Shi Tong, who were faced by a bunch of kids who, while bending prodigies, had no experience with the physical manifestation of spirits whatsoever.
I'm not saying he's not evil (although I hope he isn't), but I don't think he was behind the barbarian assault on the north or the rampage of the dark spirits just because he could pacify them (nor do I want him to be, because seriously, that's lame). For me he's still just a super-conservative preacher who seizes the opportunity of dark spirits causing trouble to impose his values on the more religiously-relaxed south.
One of the beautiful things about the Avatar universe is that it has such an amazingly rich history, something we only got a tiny glimpse of due to the nature of the main conflict in Aang's story being a 100 years war. So why
can't the pacifying technique have a precedent? It was just never accessible for our protagonists or even side characters in the stories we've seen before this point. Bending can do so many extraordinary things - controlling plants by the Foggy Swamp tribe, for example, or the Sandbenders in the Si Wong desert - so why can't some guy or girl a thousand years ago have come up with a technique to pacify dark spirits because they were causing trouble back then too, so it was recorded on a scroll for future generations to learn, in case spirits would go haywire again?