I loled so hard in the earlier scene, when you go into the facility and Alma runs and and full on Glomps you.
I was like "She glomped me...she...Oh. That's why she's chasing me..."
Also, a point to consider, the point of a 'silent protagonist' is to better immerse the player into the character, to give the impression that he thinks what you think, and just never happens to say anything. Basically character=you.
Second point, its not rape if you want it.
In my mind, Beckett and Alma will now happily raise a family on the island, occasionally slaughtering anyone who trespasses.