Responses
He didn’t use him as bait. In that situation even though Elliot was innocent he looked absolutely guilty. The duke had to do something and keep him safe while he figures out the real culprit. The duke showing favor to Elliot actually backfires because now whoever wants to hurt the duke will want to try to get to Elliot first.

Ngl if I was Elliot I would resign the next day ain't no way I can look at my boss the same way again. And the duke didn't even apologize for locking him up and using him as a bait. I would totally loose all feelings.