We do not know at which point she was Justine, She was influenced/infected Justine, She was possessed Justine.
When she got pregnant, she wasn't just Justine, HWWBs gloated about that. Hey, Thomas may have know she wasn't herself, even possessed, but because he loves her, he couldn't risk her death. He may have thought if he got by with it, Justine saved, that he could then deal with HWWBs.