During first sex with her you told her to start using pills.Sorry, I need to clarify my question. Can Lydia get pregnant again after moving into mc's house and already having a child?
I will implement an option to ask her to stop using it.. but for now, the only way is a console command:
During your play, open the console (from the main menu) and type/paste this:
SecretBirthControl=2
Press Enter, and then ESC to exit the console.
Now she will no longer be on birth control.