There was too little time. And I imagine it is hard to be that quick and lucid in breaking the rules of ATC.
Edit: I've looked it up and according to this article [0] there was only an informal agreement between Skyguide and the German counterpart DFS regarding this border region. Since ultimately only Germany is solely responsible for their airspace no such an agreement can exist and therefore the federal government (Bund) is partly to blame for the accident.
Indeed the controllers in Karlsruhe had the obligation to intervene asap even without informing the Swiss counterpart but they were instructed otherwise although there had been no legally binding transfer of the sovereign task ("weil es keine rechtlich verbindliche Übertragung der hoheitlichen Aufgabe gegeben habe"); so this was illegal. In both cases a management issue.
[0]https://www.dw.com/de/deutschland-haftet-f%C3%BCr-fehler-der...