Besides the problem with notifications that Matthew raises, there are a few problems with preventing users from commenting on their own questions, which could not be easily fixed:
Sometimes, a user may not know how to obtain information that has been requested. It's better for them to ask in a comment (which can even be cleaned up later) than to clutter the question with a series of numbered or dated (or unlabeled!) edits at the end ("running edits" as Matthew puts it). Many of us have seen this happen on a number of sites including AskUbuntu, and it's way nastier than the problem of long comment threads (which, again, can be cleaned up).
Sometimes, users will have already provided the information that was requested, and the commenter just didn't notice. A comment is really the only reasonable response in this situation. Even editing the question to make the information more prominent would not always be warranted, and would not usually be sufficient to call the commenter's attention to the presence of the information they requested.
Users would probably feel that the system does not respect them, if they cannot reply to a comment someone has made to them. And they would be right. It's one thing to restrict new users from posting comments on other people's posts. It's another if they are at a disadvantage when speaking back to people who have spoken to them. The purpose of getting new privileges as you advance in reputation is to keep inexperienced users focused on functionality they're likely to use well. Rewarding users for their contributions might be considered a legitimate justification for the system we have, too. But if we impaired people's ability to express themselves on an even keel with people who have spoken to them, then I think we would have moved into downright elitism.
New users sometimes have trouble figuring out how to properly edit their questions, or to properly undo accidental edits (like deleting most of their post by mistake). Meta is a good place for these questions but very new users cannot create questions here, and they're not likely to know to do so anyway. Simple questions about how to properly edit one's post are very reasonably and efficiently asked in comments, which can (again) be cleaned up later.
To clarify about cleaning up comments later--when a comment is no longer relevant, it can be flagged for moderator deletion for that reason, even if the OP doesn't delete it themself.