My general feeling after many years of internet use was absolutely to limit anonymity (I'm the current SciRate maintainer). Scientific discourse has its own culture, though, which is a bit different to internet culture in general. And the users seem to like anonymous peer review; we've had requests to make it more anonymous: https://github.com/scirate/scirate/issues/304
So currently I'm adopting a "wait and see" approach wrt. trolling. Stay open unless/until it becomes an issue, but make sure to crack down swiftly if it does. For the moment, we do have comment reports/downvotes and moderators.
The comments SciRate gets at the moment are pretty decent, I think because people mostly just integrate it into their existing review process. https://scirate.com/arxiv/1501.07071 is a good example. If the community were to grow though we'd definitely want heavy moderation.
So currently I'm adopting a "wait and see" approach wrt. trolling. Stay open unless/until it becomes an issue, but make sure to crack down swiftly if it does. For the moment, we do have comment reports/downvotes and moderators.