That should always be the right approach. Penalize bots that are useless, if not malicious, and the humans behind them. There are many useful bots that deserve to be rewarded.
In the end, the action taken will be against the humans behind the bots. So similar procedures should apply.
Really eager to see your Reputation system in action.
As usual an excellent comment @liberosist. Fully agree that there are many useful bots. I definitely need to mention @ anyx 's Cheetah-bot which is doing an excellent job against plagiarism.