My local paper (a paper in a smallish Midwestern city) did forgo commenting systems and doesn't seem to have suffered for it. In fact, I think it makes reading the online version of the paper better.
Their argument was more about quality, at least publically. The comments were a cesspool of backbiting and misinformed readers using the medium to make themselves heard and the paper basically said: "If you've got an opinion you want published and are willing to put your name to it, you can send us a letter and we will consider it for the op-ed page." I frankly think this was a mature way to approach the issue.
Like any other scheme to make commenting more expensive (resource wise), it implicitly makes the assumption that the value of what one has to say, somehow correlates with how much resources one has at ones disposal to be heard.
In the web era, the most important job a publisher has to ensure his site is a good one, is to write and edit content in such a way that he attracts an audience of interesting readers. Who will in turn, offer interesting comments. It is not, as may have been the case earlier, to hire the "best" journalists, to write their version of the truth. Sites that still use the latter approach, rarely, if ever, reach the level of truly interesting, simply because no one, or small group of, writer(s) will ever cover all bases, the way a whole community of interested and interesting commenters will.
I pointed this out in another comment, but I don't see why content and community have to coexist on the same site. Sites like Reddit and HN leverage the power of hyperlinking to merge the two models so each can do what they are best at: creating content for news sites and moderating and curating for social sites. I don't want to see what a bunch of wackos write in the comment section of my local newspaper. They added no value and the very few comments that did were not worth the overhead. HN has a community of interesting commentators, but it still relies on journalists to provide the basis for that community.
Their argument was more about quality, at least publically. The comments were a cesspool of backbiting and misinformed readers using the medium to make themselves heard and the paper basically said: "If you've got an opinion you want published and are willing to put your name to it, you can send us a letter and we will consider it for the op-ed page." I frankly think this was a mature way to approach the issue.