We are still looking into alternatives, but I believe we may be stuck with Disqus due (in part) to the fact that there is no good way to export/import between competing commenting systems at this time. As I am firmly opposed to losing the comments on this board, that has limited our options tremendously.
On a plus note, I have figured out how to turn the Disqus ads off and have done so.
Thank you for your patience as we struggle with this change.
Update: There is now a "link to Disqus comments" link on each thread which will jump you back to the top of the comment form. The speed of this process will vary for the individual, but it seemed a good optional addition to have since the comment box is now sandwiched between the post and the comments instead of at the bottom of the page.