Bots are already registered. I don't know the details yet but there's a procedure to apply for listing the bot on some maintained list. Most, of not all, voting bots are listed somewhere. Even if not, a procedure and a repository can be created to make that happen. From there on, it's simply the work of devs to edit the code and add something like:-

If incoming vote is from a registered bot, do not affect reputation of the author.

Translate that into code and it's done.

Thank you very much for your honest and descriptive feedback.