The proof that Stephanie was not involved in the murders...

...is that Muff's body, and no doubt Mac's, was disposed of in the lagoon instead of the ocean. If Stephanie had been involved in any way, even after the fact, Walker would not have had to hide the bodies from her. They would have put the bodies on the Iola and sunk them out in the ocean when they scuttled the Iola. There's also the matter of Stephanie passing a lie detector test that showed she was telling the truth about not being involved in the murders or having knowledge of them, but it's pretty clear from Walker's action in hiding the bodies in the lagoon that he was pressed for time and the only reason he would have been pressed for time was that he feared being discovered by Stephanie.

http://thinkingoutloud-descartes.blogspot.com/