Oh, she knew. It's not even up for debate.
From the manga, chapter 68:
Hohenheim: "Trisha, ever since I acquired this body, I've seen so much death. I tempered my sorrow by telling myself it was all a part of the greater flow of the universe. I watched in silence, as humanity repeats the same mistakes over and over, never learning the lessons of history. I've seen my closest friends grow old and die in the blink of an eye. Familiar places have been rendered unrecognizable by the passage of time. There were still many beautiful and mysterious things in the world I hadn't seen. Each fresh encounter made me glad I had acquired this body and lived on. That's what I thought.... Trisha.... until I met you, and these children were born. I never get older, and yet my sons, who share my blood, continue to age and grow. Suddenly, I'm terrified. I think to myself, 'Yes, I really am a monster.'"
"Humankind cannot gain anything without first giving something in return. To obtain, something of equal value must be lost. That is Alchemy's first law of Equivalent Exchange. In those days, we really believed that to be the world's one, and only, truth." -Alphonse Elric, Fullmetal Alchemist (1st series)