As you know, Google just updated the search results and PR. This has worked out great for me and if you check out the Author's main page you'll see tons of comments that have been paginated, are recognized by Google and rank well.
Since installing this plugin, Google now recognizes comment pages that are deep, deep within my site.
You say that it generates urls for each page, and yes, it does generate unique urls for each page of comments, but that is not duplicated content; it is pagination.
Pagination allows a post with 1000's comments to be split into multiple pages with unique titles and urls. Nothing is duplicated, only split up.
Perhaps you can be more specific and provide a website address and example - visit the author page, go to the bottom and send me an email and I'll take a look at your site.