Because we saw in flashbacks that Three had a relationship with the woman who was in stasis and did not want her to die.
From the Wiki site:
"Episode Seven" Bruce McDonald Robert C. Cooper July 24, 2015 TBD
The crew manages to gain access to the ship's secret room. Inside, they find a stasis pod carrying Sarah, a woman from Three's past with a deteriorating disease, and an android named Wendy, who is programmed to perform a wide range of activities, including cooking, games, and sex. As Sarah fills Three in on their history together,
Wendy's programming is replaced with orders to destroy the Raza by Cyrus King, a man who wants revenge on the crew and knew the android would be activated. During the flashbacks we see Sarah caring for Three after he is wounded. It shows Three apparently falling in love with Sarah and becoming very close. Though Three does not consciously recognize Sarah because of the memory wipe, somehow a part of that love comes through which is why he wants to protect her. He knows the only way to keep her alive is to put her back in stasis as the disease is incurable.
Additional plot details at:
Dark Matter Commentary Site