I think we could easily redesign a few aspects of the UI in such a way that the user is able to do what often seems to them to be the right thing while learning how we work.
An example of the sort of thing -- saying "Thanks":
Users want to say "thanks, that was helpful" but the model is to use the upvote button rather than comment. If we say "don't post thanks, use the upvote" it does seem a bit rude.
But what if the upvote button actually did say thanks? Then we're not saying "you're doing it wrong" we're showing them how to say thanks before they even think to do it.
So a nice way to guide new users to use upvotes to say thanks would be to literally label the upvote button to say "useful, thanks" (just above would be clearest) -- it would appear as soon as they can use the upvote and continue to appear until the time when they have upvoted at least 3 times.
[To reinforce this sense of "I'm sending a thank you", on clicking upvote, the "useful, thanks" could be animated to drift up and fade into the ether.]
Similarly, the accept-check should be labelled for brand new users, until they have used it a few times -- e.g. "this is the most useful answer"
Such an approach -- of showing new users how to do what they want to do, like say thanks, makes the site friendlier, saves the sometimes confronting nature of being told "we don't work that way, we work this way". Help people to see how to do what they want without having to be told, and they'll be happier.
At the same time, if we can have bots cleverly helping to detect spam, why can't we have bots do the much simpler task of identifying "thanks" comments, and (after a few days) greying them out, and then after say a week or so just autodelete them. The person gets to say "thanks", the clutter is small and temporary and nobody needs to say "you're doing it wrong" because it no longer would be wrong. If you want to say thanks, you can do so but it will be a temporary comment, not a permanent one.
If people vote to delete the comment, these go through but are applied through the same grey out after a few days and eventually-delete scheme; bots could speed such an identification process up as they do with spam already.
Simple UI changes like these would make the site friendlier for new users without actually changing much about the experience for more experienced users.