Maybe she wrote something in which she suspected Stern was involved in Daniel's death.
I just don't think she would be hangin with him as much as she did if she thought Howard killed Daniel or if she felt that she was in danger. It doesn't make any sense at all.
I can think of a scenario, where accidently Daniel drank ANS methadone drink and she felt responsible and knew that Howard knew what happened. He could have also planeed that to happen and make her feel like she was the guilty party by switching drinks.
He then had even more control and said if we get married we don't have to testify against each other or something along that line.