The major reason why low rep people are not allowed to comment yet, is that comments are not reviewed, so possible unwanted stuff in there is less easily detected (normally only the poster of the Q or A on which was commented gets notified). That is why there is a very small threshold of 50 rep before you are allowed to comment.
If a new user instead misuses an answer area as a comment. It clearly indicates (s)he has not taken the time to get familiar with this sites purpose and rules of behaviour. Whatever the value of the answer as a comment, the poster should be notified and the answer removed or, at the mods discretion, converted to a comment.
In the particular case you indicate, the "answerer" was the Question's OP. And (s)he could have commented below the Question, or edited the original Question if more appropriate. That someone comes to U&L with a question and expects others to invest time to answer, without investing the time to learn how to properly use the site themselves is something that worries me a bit.
What you should do is flag the item independent of the posters reputation. In addition down-vote it if the answer-comment is not useful, you will get the rep you loose for down-voting back, if the answer gets removed/converted.