The Submachine doesn't control us. In a way, Mur did - We followed his instructions to get out of 2, 3, 4 and 5. However, if the Submachines controlled us, how would we able to get out of any of those puzzles in the first place? It would trap us there, as it's assumed it's trapped the other "The Players."
Then why did the end of the Game say this?
You have collected the ancient crystal of wisdom...
wisdom gives you endless power to find your own path in life...
may it serve you well
I take it meant the person we'er playing had been trying to gain control over his own life.