Seeing that much of Voyager in later years was shown out of production order, I always assumed "Renaissance Man" was written and filmed before "Author, Author". So Janeway isn't punishing him because she still doesn't see him as "real" and it's absurd to her to punish something she views as a machine. I'm not sure the EMH can be held in the brig. Couldn't he just walk through the force field or transfer his program to another room? He would have to be willing to accept punishment I assume, if not other than deleting his program how would you stop or contain a being of light and computer pathways?