Science

I disagree that that's necessarily a problem and I believe the problem only arises when looking at the perspective of no free will from the basis of the opposite side. The colloquial idea of 'punishment' comes from most people's current perspective of free will; if there's no free will it isn't punishment, it's just solving a problem.

As an example of an analogous perspective irrespective of free will, take chemistry: Say you're reacting two substances which oxidize when exposed to an atmosphere, if you want to react them in their non-oxidized state you have to do so in an oxygen free environment so you pump in pure nitrogen to displace all the air. The air has no free will to choose whether or not it'll react with the substances and ruin your intended reaction so it'd be silly to say you're punishing the air for something it has no choice in. You're treating the air differently simply because it's problematic, not because you're trying to teach it a lesson.