I go to zoos somewhat frequently, mostly the National Zoo in D.C. and Omaha zoo, both well-regarded. Neither or them cut the tusks of their elephants. I wouldn't expect any zoo would cut the tusk to prevent them from harming one another, because elephants are perfectly capable of killing each other without the tusks. There are a couple reasons why you might have seen that, aside from animal cruelty.
1. They were rescued from another facility that cut the tusks.
2. The tusks weren't actually cut. You don't elaborate on what you mean by "cut," perhaps you mean you see the large base of tusks but very short and clearly cut by a saw or something. But if you just mean the tusks are very short or absent, that's actually somewhat common, especially in Asian elephants.
3. Depending on where this zoo is, the zoo could have been worried about poachers. There have been incidents where poachers have broken into zoos and killing elephants and rhinos for their ivory.
In response to your question about capturing elephants in the wild, my response is that the primary moral imperative here is the preservation of the species. If the limited capture of a small number of elephants was being done as part of a plan to reintroduce elephants to a region where they have gone extinct, I would be in favor of that. If these elephants were going to a respected zoo as part of a breeding program with goals to re-vitalize the species, I would be in favor of that. I would even consider arguments that taking a few elephants to a respected zoo for research or education purposes would be better for the long-term survival of the species, though I generally reject that idea because there are a sufficient number of elephants available for rescue that are not capable of entering/returning to the wild.
As an example, the African elephants at the Omaha zoo previously lived in a wildlife preserve in Swaziland. But a record drought threatened their survival. By moving the elephants to a zoo, they reduced the elephant population in the park, leaving enough resources for the other animals in the park to survive. http://www.omaha.com/living/zoo/year-later-elephants-have-ma...