Legalmania, the speculation is that the boyfriend, being a police dispatcher himself, stated suicide on the 911 call because he was aware that if he said gunshot the media would be all over everything right away.
I believe the coroners report stated that Molly had "well under the therapeutic amount" of an anti-anxiety med, and also a therapeutic amount of benedryl in her system.
Molly had been depressed and suicidal in the past-LE cited a suicide note found in her bedroom at her parents house (which apparently was searched quite thoroughly, unlike the scene of her death). LE has used this note to push the suicide theory, however Molly's family and friends state this "note" was an undated page in one of her journals from two years ago.
There are also a series of texts in question-in question because according to Molly's father on the justiceformolly Facebook, Molly's phone had been tampered with to change the time zone. Interestingly, police couldn't run forensics on the boyfriend's or the roomate's phones because they wouldn't "sync up" with the analyzing software. Fwiw, the boyfriend's father is a forensic IT analyst for Carbondale PD.