Before I start railing on Megan, I want to say that she is human, and therefore imperfect. Also, the touchy issue of falling in love with her source, Mike, is not acceptable, but understandable. Humans form bonds with other people, and I don't think it was wrong she liked him, just wrong she continued to do the story in that situation.
And, I do not think Megan can be blamed for Ms. Perrone's suicide. Ms. Perrone gave her the information, and while she didn't want it published, it was very relevant to the story, it was an alibi! We don't know exactly what Megan said in the paper, but if she just presented the facts, then there was no ethical dilemma. Journalists' job is to give the facts in an accurate and fair way, and sometimes people don't like the facts, but that doesn't make the news industry evil.
Now to the railing. There were many ethical issues, but I think the biggest is that Megan was not accurate, and she assumed. Journalists should never assume. Whether by preconceived ideas or whatever, Megan assumed what she thought were valid facts. For example, she assumed when she wrote the first story that Mike wouldn't respond or want to cooperate, and she did not get his side. That is so irresponsible for a journalist, its embarassing. She also assumed that everything in the file she stole was correct and valid. It seems she should have done better backgrounding, and checked other sources before publishing that first story. She also assumed that Ms. Perrone, at first meeting, was Mike's girlfriend.
As a personal moral, I think all the alcohol Megan consumed while on the job, finding the story was also irresponsible. It impairs judgement, and that is not a good thing for a journalist. Also, her continued 'meetings' with Mike were mixed between personal affairs and work, the story, and that is not right. She played him for the story, and vice versa, and that also impairs credibility and judgement.
I don't think Megan ever got it right. She always missed the mark because she let ethical dilemmas overrule her journalist's judgement.