It was one of the ideas she had come up with.
Brendan was worried he would act wrongly out of impulse and hurt Deirdre as well as the baby in her womb. Hence, Deirdre had given the order to release Sam from the organization.
Firstly, she did it because she owed it to Sam. She was supposed to look for an opportunity to free him.
Secondly, she did it because Sam was the only person she could trust. He had helped her so much in the past.
"I've rested way too long in the organization, so I rush