What seems more likely is that the murder-for-hire thing is messier than the broader, abstract things he was charged with, and they had him dead to rights on that stuff anyways. Without meaningfully contesting and refuting the murder-for-hire stuff, it's relevant conduct for the sentencing; it did the work the DOJ needed it to do.
The big issue in these discussions is the idea that the murder-for-hire stuff was prejudicial --- that it wasn't a part of the case, but was allowed to hang over the case to taint the jury. But that's clearly not true; he was indicted for it, twice, in the SDNY case.