That and at one point she did approach Jack to kill Ben on the operating table.. This can't be ignored either.. We know she has many reasons to hate Ben.. I still do not trust her but we have to go with the facts that we know.. She wants off this island and Ben will not let it happen until she finishes her work... He said so

__________________
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.