The Lower the amount of reputation needed to comment question has been bumped to the top (a minor grammar edit on an answer).
It made me think that a better solution would be to have early comments get a popup window saying something like
Are you sure you want to comment? Comments are for asking for clarification on existing questions or to suggest improvements to answers. If you have an alternative solution, please post an Answer. If you have a question of your own about the subject, consider Asking a Question. Please avoid comments of the form, "Me too!" or "Having the same problem!" We have answer and question voting (link) for those situations.
Implement the buttons and (link) appropriately of course.
It's possible that there should be different messages depending on whether the comment is on a question or an answer. I'm not sure whether a single message or two more specific messages is better.
New users come to a question, they can see comments, but the only place they can type is in the answer box. Is it any surprise that they use it incorrectly? So replace the text box with a button that says "Answer" until reputation is 50 or 10 or whatever. This won't impact people who already know the site (as long as the reputation requirement is below the 101 that users currently get on later site registrations) but will make it more obvious to new users that they are answering and not commenting.
Note that this could work either with a lower comment threshold or as things are now.