Yea I don't think that Mr. Linus is her biological dad, just who she has been told is her dad..

Danielle was pregnant when she arrived on the island. I THINK she said somewhere between 5-7mo.. She said that she delivered the baby girl herself and within a week the others had come and taken Alex...

Remember Danielle was married and on the research team with her husband and the rest of the team.. So Mr. Linus could not be the biological father

__________________
Please don't give up, Des. Because all we really need to survive is one person who truly loves us. And you have her. I will wait for
you. Always. I love you, Pen

DESMOND: I love you, Penny. I've always loved you. I'm so sorry. I love you!
PENNY: I love you too.
DESMOND: I don't know where I am, but--
PENNY: I'll find you, Des--
DESMOND: --I promise--
PENNY: --no matter what--
DESMOND: --I'll come back to you--
PENNY: --I won't give up--
BOTH: I promise. I love you.