He's aware. He modeled that process in sufficient detail to think of it as one possibility among others, and prompt her removal to a scry-screened area after she got a headband, timed for when she wouldn't have prepped spells yet.
He knows that what she thinks while under Detect Thoughts will end up not being something that can bind her real self. She doesn't need to think about whether or not her real self is a being that will keep oaths.
What he might hope to accomplish, by this, is, first, to see if she's directly outgrown the power of a geas to bind her without her even trying; and, second, more importantly, that Carissa have obtained a true understanding of his model of the universe and herself and himself as he truly sees those things, based on her seeing his thoughts, and his seeing her seeing his thoughts.
If she decides to betray her oaths and him, after the Detect Thoughts ends, she'll at least be doing it based on true information that would pass an Imitation Game test. She'll be doing it based on correctly knowing the structure of oaths, and what's at stake there far beyond Pharasma's Creation.
Her thoughts of him have seemed to him, from time to time, not just unjust but inaccurate. If she betrays the Algorithm on the basis of a wrong model, that's a farce and not just a tragedy. That's what he'd be hoping to prevent.
He wants her to have the option of seeing reality, himself, and herself, as he would see them. He wants that understanding to be inside her, when Detect Thoughts ends, and she actually grows into herself. If she throws it away then and shatters her vows, then that's how the story ends, he supposes.
Carissa has not - as he understands all this - read his mind directly since she met him at the Worldwound, let alone with INT 29 at which level she might begin to understand what she saw.