Yes, they are allegations, but she didn't make
the allegations - the police did. So, everyone knows she didn't "sanction" them, and has no need to apologize for them.
What she needs to say she didn't sanction is the actual criminal acts that people under her authority have been convicted of. Note how she carefully did not apologize for *those*.
The PI's apology is also a magnificient piece of apologizing but not really:
"I want to apologise to anybody who was hurt or upset by what I have done. I've been to court. I've pleaded guilty. And I've gone to prison and been punished. I still face the possibility of further criminal prosecution.
"Working for the News of the World was never easy. There was relentless pressure. There was a constant demand for results. I knew what we did pushed the limits ethically. But, at the time, I didn't understand that I had broken the law at all."
In other words, a big dose of "I'm sorry you feel that way. Now leave me alone, because I'm the one who's really
suffering. How was I to know hacking into phones was illegal?".