Everyone knew that Alison and Beth had a thing. It was simply common knowledge, it was accepted and nobody bothered to question it. It was never really spoken about, no one told Sarah and Felix when they got involved with the world of clones, they just knew, or found out for themselves. It was in the way that everyone carefully avoided Beth's name when Alison was present, in the way that Cosima would smile thin-lipped and apologetic at Alison when someone slipped up and did mention her name.

For Sarah though it was mostly in the way that Alison treated her, especially in the beginning. How she sometimes snapped at Sarah for seemingly no reason (she sounded just a bit too much like Beth) or how she often couldn't quite bear to look at her when she was being Beth (the face was the same, the woman wasn't) and how she looked at Sarah sometimes as though she both wanted her and hated her at the same time (she did). But nobody says anything, no one tries to console Alison, not that she'd likely let them, and no one questions her behaviour. It just is. Alison and Beth were together, they loved each other. That's it.

It's only when this truth dawns on each of them individually that all of these things begin to make sense. It's only at that point that Sarah realises that she can't play Beth forever, not only because she's really quite shite at it, but also because it's killing Alison.
Sarah remembers vividly the moment when she realised that Alison and Beth had not been all that they seemed.

"The truth is I barely knew Beth"

Sarah knows it's a lie as soon as the words have left alison's lips. She's saying one thing but her face is saying another. Within that tightly maintained posture and rigid but emotionless expression is a different story. They might not have known each other like most other couples might, but in that moment Sarah knew that Alison certainly knew more of Beth than Cosima ever had, perhaps even more than Paul and Art and Angie ever had.

It was right then, with Beth Childs' gun in her hands and the woman's grieving lover stood beside her that she felt truly guilty for the first time about inhabiting Beth's entire life without ever worrying about how anyone else may feel about it.

After that she doesn't push Alison any further for information about Beth, she shuts up, fires her gun and gets right back to business. Just like Beth would've done. Alison's grieving, and she made it pretty clear that Sarah wasn't going to be the one to comfort her, not when she's dressed in Beth's clothes and Beth's voice and Beth's life anyway.

Nothing was ever really said about Beth, at least not the real Beth. And certainly nothing about Beth and Alison. It just was.