1) Governor Christie was still in office - even though Democrat Murphy had won the election. To at least some jurors, the potential that Christie might name a replacement could have been a factor
2) More significantly, the Supreme Court had overturned the convictions of Bob McDonnell, the VA Governor, who had accepted goods from people he helped as governor, who - like Menendez - he called "friends". Before that decision, the case against Menendez was stronger.
That said, Greenwald should not have said "just barely escaped" -- because it is not accurate. I assume the point that he is making is that where Menendez was not convicted, the investigation and the trial did expose ethical lapses. He was not found INNOCENT, he was was found NOT GUILTY. Months ago, when visiting the area we lived in for nearly 4 decades, I ran into some people I knew from having volunteered as a Democrat years ago. I was disheartened, but not surprised that there was no real challenge. Let's just say that for people who favor "good government" Democrats, NJ can be frustrating.
It may well be that Menendez made it clear he would fight tooth and nail and certainly would not decline another run. The state party would then face an expensive primary battle with a damaged winner -- or tacitly back the incumbent. For Menendez, stepping down would have effectively meant that his bio would end with the trial, the not guilty verdict, but then an end of his career - giving resonance to the idea that he had acted unethically. Running means he will likely be Senator for another 6 years, hopefully we retake the majority either in 2018 or 2020. Then, Menendez would be a high ranking Senator, with seniority who would be the chair of a committee (maybe the SFRC as before). His personal story still has this negative, but it will be balanced by any later accomplishments.