As far as I know, the karma lost through down-votes on a comment is permanently lost rather than returned/refunded when the comment is deleted. Even if I'm right, your point still stands, since deleting a down-voted comment would put an end to further down-votes, so it's possible that some may delete comments to save face/karma. Similar could be said for editing.

Unpopular opinions are always tough situation. Part of the problem stems from "up" and "down" votes meaning different things in different contexts. For example, up-voting a submission is a way to say "thanks" for submitting it. This usage is problematic since the opposite of "thanks" really doesn't exist. The typical negation "No Thanks" is not strong enough, and "flag" is far too strong. For submissions, there is no down-vote. In contrast, votes on comments are often used differently, such as an up-vote being used to show "agreement", and a down-vote being used to show "disagreement". The contrasting usage of votes results in both user-centric context and submission/comment context influencing what each vote means.