I'm a (fairly new) moderator on Raspberry Pi Exchange and everyday there are numbers of answers rightfully flagged as non-answers because they are essentially comments left by people with not enough rep to comment. I go through them and decide whether to just delete them or turn them into actual...
The work around, if you don't want to auto-penalize someone when converting something to a comment, seems to be to do it via the page (not the flag queue), then decline the flag. It only applies to "low quality" flags; my main concern are ones set by "Community" simply because they are short (and should be comments) but really shouldn't incur a penalty.
Sounds like a complicated hack to a fundamental issue. Beginners with no rep can't comment and therefore post badly phrased answers which in turn are penalized. Not saying that it is right, actually I am d'accord with your considerations. So why is it that beginners are not allowed to comment in the first place. Sounds to me like that would solve the issue (and probably has been heavily discussed before).