A lot of people seem to be mislead about how this band came about. It started as a side-project between Piet, Thomen, Emil, and Jens while Thomen was still in Blind Guardian. Everything for the first album was recorded before Thomen had announced his departure from Blind Guardian. Piet did just as much (if not more) of the songwriting on Dreamland Manor as Thomen.
When Thomen took 2006 off, he put the band in a pickle as far as touring went. They managed and carried on with Thomas Nack as a stand-in drummer. When Thomen "came back" earlier this year, Savage Circus planned more shows, but ended up having to cancel some from Thomen being sick. When the band starts getting a reputation as being risky to book (like Royal Hunt), it's a good idea to do something about it. Thomen couldn't overcome his problems fully at this point, so the best course for the band was to let him go so he could sort out what he needs to sort out.
There is, of course, a lot more going on behind the scenes, but this was really the only option that could keep Savage Circus alive. There weren't any ill-feelings towards Thomen or vice-versa; it just wasn't possible to continue on with Thomen as the drummer.