Here's a speculational theory I haven't seen explored, so will toss it out...
When Matthew questioned Lily as to her motivations, and she basically told him free daycare and housing, he said he wasn't a true believer either, but yet we KNOW Matthew has a grand master plan with Isabelle. If he's just a slick PR Marketing glitz guy out for fame and money, what then is the plan? Or was Matthew meaning he's not into the Cultic Religional end of it rather the pure Science? He hasn't enjoyed defending the Nova Group, and he's no public-eye smooth Jordan, rather a behind-the-curtain Administrator-At-Large. But yet, he does believe in something, what, we aren't yet sure. I think he just meant he doesn't believe in the Key System.
But almost right after Lily said that...she was transformed into an old lady, and later died. Did Matthew "move her out of the process" as she would be a bad influence on Isabelle? Why did Isabelle need to grow up so fast? (Well, outside of the Laura Allen incident and the obvious acting problems in dealing with babies as actors). Still some motivational need on Matthew's part as for the acceleration, assuming he caused it.
What was Lily's power? Maybe she had NO power herself, rather her power was in her pregnancy, so once the kiddo's born, if Matthew can accelerate the process, taking over the nuture role and getting Isabelle into full awareness, Lily's seriously expendable.
Hence Matthew "killed" Lily, which may or may not be a good thing. Matthew seems of the 'ends justifies the means' ethical lapse sort, but then if he's Futureman or at least in contact with such, making the puzzle pieces all fit together to keep the human race alive in the future, can be somewhat justified. Big scary seemingly contradictory ethical questions, kill so others live. Choose death, yet choosing life. Peace by War.