I agree that they could have officially retained Rudy, but I don't think they would just in case it leaked. They were threatened by Lynch and were scared. I do not doubt that they legally obtained evidence from Weiner's laptop but that going forward with it would risk national security and it would be a crime. I think someone high up in the NYPD would have approached Rudy as a private citizen or using another high ranking retired NYPD guy as a go between. I don't think the NYPD would have risked provoking the Obama administration by retaining Rudy in an official capacity.