As others have said, de-federation should really be the last resort for the most egregious of actions. The bot serves a well-intended purpose, even if it’s something I would never use.
What if the bot was hosted at .ml or .world? Would de-federation even be on the table?
My vote would be to leave it up to the users for now, though I don’t fully understand what, if any, performance impact the bot account might have on other instances. Is traffic from that instance excessive? If performance was a factor, then at most I would vote to ban the bot account until the platform has more options to manage such things.