The game is littered with monsters capable of hypnotizing women into having sex with them and humans that got corrupted/infected into becoming a monster. So that doesn't really prove she had a normal human-to-human intercourse. And from their dialogue, the pregnant woman must have been aware something was off about the man she chose to have sex with but she said screw it and decided to take the risk.
Again, if any pregnancy results in abomination brooding due to corruption in that region and everyone knew about it, there is no reason the pregnant woman's brother to be surprised about his sister's abnormal child or Lilia suspect the woman of being pregnant with abomination.
Yeah, the pregnant woman's brother mentions this bit in their dialogue and he also points out how both Lilia and Hannja are different from them. But again, that only hints at the corrupt priests you run into later in the game. It doesn't really prove any sex results in abomination brooding.