Guess I like Marshall for her because I'm married to my best friend.
Yes, and probably you are in a healthy relationship with your best friend.
But, poor Mary is so emotionally messed up with abandonment issues because of her dad, un-reliability issues having an alcoholic mom, that she has intimacy issues because of all of it.
The very first lines by Mary, in this episode, during her narative voiceover, she talked about her dad, once again. About him leaving her. He's like an invisible character in the series, and always a deep part of Mary's life.
I know Marshall would be there for her - he'd lay down his life for her. But if/as Mary starts to feel feelings for Marshall,
she'd just screw things up and push him away, and all that, as she'd be too afraid of the one person who IS there for her, may up & leave like everyone else has done. IMO, even if Mary woke up & realized she has feelings for Marshall, it would be a long, long time for her to be able to trust her heart to him, even though rationally she knows he's always been there for her.
That's what I meant about her needing Marshall as simply her best friend. Who would she have to turn to if she messed up her relationship with her best friend/lover? Her self-absorbed, alcoholic
mom? 
Right now, Mary really doesn't have anyone else.
It looked like to me that the actress who plays Brandi is/was pregnant. I assumed she was going out on maternity leave.

I totally missed that. Hmmm,

I thought all those cell phone calls were from their dad. That he finally made contact with Brandi to find out how Mary was doing in the hospital. And now Brandi is going off to spend some time with him and get to know him. And she'd return for guest spots, someday, (maybe with the dad?) when Mary is least able to deal with it all.
I don't remember how the stars of the show were billed last season, but when I went to watch the beginning of this episode again at 1am, I noticed that Lesley Ann Warren & Cristian de la Fuente (Rafe) and Allison Janney were all billed as "Special Guest Stars," not as regulars of the show.