If you look at the e-mail notification you get when you get a comment, there's a very nice link that highlights the comment and shows a reply text box ready to go. Why they didn't include that in the "inbox" view, I don't know, but might be worth looking at.
Don't disable comments on the videos. I can only speak for myself, but when I randomly find a video with disabled comments, I'm either thinking the person can't take criticism, or if there was a forum signup link, that the person was a bit obnoxious. In either case I would ignore that person on principle. I may be a bit extreme in this regard, but YouTube comments are great for people who found one of your videos randomly through the related video function, which I'm assuming is a lot. (Dave, you have access to these statistics.) You might argue that these comments are all useless anyway, but you can just as well let them have their fun over there. These are the people who pay part of your paycheck.