I was stuck with the problem, that i needed to transform the geometries within a featureclass, that means no new featureclass could be created.
Everything in arcobjects worked fine till i wanted to stop the edit session, which took more than an hour for 10'000 features. Using updatecursors or just storing features did not make any difference.
Finally i found the simple solution: I had to drop the spatial index before doing the transformation, and recreate it afterwords. Now the stopEditing operation takes around a second.