Suggestion: flesh out this idea a bit more, write a top-level post about it, and see if the community sees value in establishing a social norm that wrong-headed comments in that post's thread will not be karmically punished as harshly as they might be elsewhere.

You may get a different reaction than you're hoping for, but if you do you'll probably learn why in the process.

The LW platform seems to have a fair bit of flexibility in it, as evidenced by what people choose to do with a small number of "special" threads (cf. my recent edits to the Wiki) such as the Welcome, Where are we or Issues threads. So it should be possible to do quite a bit of innovation without actually having to write any new code. (Perhaps an additional sidebar specifically for these "special" threads would be a good idea though. They aren't obvious to find for a newbie.)