Operant conditioning isn't actually harmful, as long as you're not operant conditioning your kids into doing harmful things or into not doing important things.

Well it seems to go against my values. I want my kids to think for themselves, not merely be executors of my authoritarian commands. I am not their boss.

Children are not small adults. There's a point in their lives when not throwing temper tantrums in public is what you want out of them and they're just not mature enough to negotiate with reasonably. This is also the age where hopefully you're going to have to install some sort of conscience, since kids aren't really born with one, either.