Have a look at this comment, especially: https://news.ycombinator.com/item?id=11504522

Essentially, this has nothing to do with "regarding separation of powers", since the law in question requires "und die Bundesregierung die Ermächtigung zur Strafverfolgung erteilt", i.e. "that the federal government gives the courts authority to prosecute". Without order to prosecute from the executive, the judiciary would have no legal grounds.

It would have been in line with both the word and spirit of the law if she would have denied this authority.