The quality of ontologies and their alignments is crucial for developing high-quality semantics-based applications. Traditional debugging techniques repair ontology networks by removing unwanted axioms and mappings, but may thereby remove consequences that are correct in the domain of the ontology network. In this paper we propose a framework for repairing ontology networks that deals with this issue. It defines basic operations such as debugging, weakening and completing. Further, it defines combination operators that reflect choices in how and when to use the basic operators, as well as choices regarding the autonomy level of the ontologies and alignments in the ontology network. We show the influence of the combination operators on the quality of the repaired network and present an implemented tool. By using our framework together with existing algorithms for debugging, weakening and completing, we essentially provide a blueprint for extending previous work and systems.