The actual father of the kid may be...
Doktor Bernhardt!
It's shocking but he was an evil genius.
While Rachel was feeding the doctor (at 00:57:38), he said exactly these lines:
"One of the greatest regrets of my life is that we were unable to have children. My wife would have been a wonderful mother. You should try lemons, for the morning sickness. They say it helps."
Morning sickness is usually suffered by pregnant moms so the doctor gives a hint she is pregnant.
He is talking so sure like he somehow put his own sperm in her vagina !
Also the talk between Stephan and Rachel on the beach (at 01:18:36) is ambiguous:
Stephan says "If I could go back, Rachel, I would change it all. But there's one thing I would never change."
Stephan looks at Rachel's daughter playing on the beach
Rachel says "She isn't going to find out."
Sounds like they are talking more about the truth about her actual father rather than the truth about the mission.