If you're a US felon trying to make a life, thinking of employers' motivation as being to punish you would be inaccurate and probably counter-productive. I don't quite agree with your characterisation of employers' motivation (I think corporate management is as uninformed, irrational, and prone to post-hoc rationalising of unthinking reflexive behaviour as is any other sector of society), but that's a side issue here. If you have a criminal history, and want to get back on track, you have to deal with potential employers as you find them.
If you're instead concerned about policy & intent on analysing the system as a whole, employers' reluctance to hire is absolutely part of the criminal disciplinary system, interacting with many other parts (eg. cultural attitudes towards criminality, levels of legally required disclosure of criminal history, legal classification of crimes, etc, etc). In a society (for example) without permanent public records of criminal convictions, or where they are rapidly expunged, and with no duty to disclose criminal history, ex-cons de facto receive less punishment. Whether the more or less punitive system offers the best balance of goods for society is a topic for debate, but that employer reluctance to hire acts as part of the punishment system is just a fact, regardless of employer motivation.