I completely agree with your first and third points; so, I'm not going to say anything about them save a query about the current comment-hiding algorithm. Does it not already take into account comment flags?

Your second point is going to be tricky, as [Skliwz][1] has stated, because people will be able to use their knowledge of the flag status of the comment in order to negatively impact people. I'm definitely not going to state that you couldn't expose the flags but I think there might be another way to attack the problem.

The problem, as I see it, is one of perception; the perception that Stack Overflow is rude and the perception that no one is doing much about it. Part of Stack Exchange's ethos was that many hands make light work (I can't find the blog post ☹). Currently, however, the ability to flag comments isn't widely known and it's not possible at all unless you have over 15 reputation.

Stack Overflow has almost 2.4m users of whom 2m can't even see that you can flag a comment. It has 6.6m visitors a day, it implies that 6.2m people don't realise that the site does _anything_ about the "rough tone".

Why not expose the ability to flag to everyone? 

This would create a different problem; a multitude of flags. However, this can be dealt with by being deprioritising them slightly. A single flag from a passer-by wouldn't need to take top priority. However, if multiple passers-by flag a comment (or post) then it means something and attention should be paid to that indication. Something being deprioritised doesn't mean that it should never be dealt with... just that the current mods might hurt me if I suggest adding hundreds more flags to the queue that they'd have to deal with.

In the same way that flagging can auto-delete now, there's no real reason why an unregistered user couldn't flag a comment and, in combination with registered users, delete it. They couldn't do it themselves or it would be too easy to get rid of everything.

Most importantly, it would give the impression that Stack Overflow _does_ care and is willing to do something.

[1]: http://meta.stackoverflow.com/a/213698/179419