The Reds were punished regardless, they're forced to keep a guy they were looking to move for a kings ransom or they accept a massively devalued offer due to the allegations.
Either way, Chapman still makes a living and is in no way "robbed of a career."
The way it played out...sure. But they got SOMETHING of value. Not as much as they would have, but something. Your suggestion was they get NOTHING. It also forces the Reds to run their organization contrary to their needs and goals, at this point. Which of those two scenarios is MORE punishing?
The alternative was keeping him, and shoving him somewhere in the organization to NOT produce anything, to NOT maximize his value going into FA AND not getting ANYTHING for him.
So, the Reds get punished AND Chapman is, realistically, robbed of his career.
Again, I'm not seeing any "moral" reason not to do the deal....and saying the Reds SHOULDN'T do it just punishes them...or potentially robs Chapman of his career...based on allegations of a questionable nature.