You should've indeed called for the FA. If she took the windownseat and stayed in that spot, without bothering you, it'd be just a minor nuisance and you'd forfeit your "poor mans business class bed". However, the way she behaved should land her in the penalty box at the back of the plane.

Something similar happened to me on my UA SCL-IAH flight. 2-3-2 config in y+, I had a window seat and seat next to me was empty when taking off. After dinner, I feel asleep (redeye flight) (with the seat next to me still empty). Low and behold 2 hours later, I wake up and THERE IS ACTUALLY SOMEONE SITTING/SLEEPING NEXT TO ME.
I was too drowsy and dumbfounded to do anything (and eventually fell back asleep), plus I couldn't find the "ring FA button" (apparently they're on the screen, not next to the overhead nozzles), but next time I sure as hell will voice my displeasure, plus boot the pax out of the supposedly empty seat.