I am sorry that you had a less than enjoyable experience on Costa. I had similar issues with their customer service issues during our Med. Cruise on the Concordia. It seems some of the crew enjoys offering challenges to their guests and are unwilling to provide the level of customer service afforded by many of their competitors.
There are effective ways of dealing with lingering cigarette smoke in the staterooms. Had they responded with an ionizer, which would actually clean the air in the room and removed the offending smell rather than sending someone with a scrub brush, you might have been a happy cruiser. Instead it appears, they chose to make things difficult and inconvenient.
My advice would be to contact the people who organize your holistic tours and share your experience. Ask them to try to stick with more mainstream cruise lines, since the "Italian cruisee experience" is not conducive to a holistic experience.
This situation could arise on any ship. But it should have been handled differently.