Strictly speaking, SXF isn't the LCC airport of Berlin. Sure it is well served by EZY and FR but there are legacies there too and of course the airports of that city have generally enjoyed equal status in the past unlike say LTN or STN to London, and of course is a by-product of Berlin's history.
As for Thomas Cook, it could have handled the situation better but I think the back lash (understandably) has a very emotive maternal undertone to it and ultimately people have short memories. In literally two weeks it will all be forgotten about. I'm sure Cooks will have learnt a lesson.