Valuable conversations can extend from comments that are already negative.

If a reply to a downvoted comment is not downvoted, replies to that reply are not punished, so good subthreads are unaffected.

-3 is also not that negative.

5 Karma points is not that much as well, so if it's really worth replying to, it's possible to continue the conversation. It's usually not worth replying though, and when not feeling any cost people would ignore that consideration, giving fuel to bad conversations as a result. The motivation I agree with is to stop bad conversations, not necessarily replies to individual bad comments, which is just the means.