One would have thought they would have told you beforehand that they would have to charge you for it.
Sad to see BMi stoop so low especially with a business class customer. Must be embarrassing for the crew I imagine. Although they should have offered you a choice first - if there was a choice in the first place that is. Regarding not checking your bags through it must have been because you were using separate tickets as jamesie_version1 explained.

Worth sending in a letter though I would say.