After emailing with Bruce, I realized a few things:
1. He was trying to reply to a comment from the Dashboard of the blog. When a blog owner is in the dashboard and looking at a submitted comment, there is a reply button there, and that's where the problem was.
2. Since replying on the frontend is presumably how most users will reply to comments, I'm not certain that we need to debug WPMu on this point. Instead, we should produce documentation that makes clear how to respond to comments on the frontend.
3. What Bruce really wanted to do was to have threaded comments, which would allow him to have his reply appear directly under a submitted comment. I showed him this post about threaded comments on the WordPress blog.
This issue appears to be resolved, so I am closing the ticket. Bruce, if this crops up again, or if you don't agree that the ticket should be closed, please submit another one. Thanks again for helping to improve the Commons!!