I can't say I care for that wording. Would you say the same thing to someone who told you they were childfree-by-choice? It's the kind of statement that can quickly land you into eHell.
I think simply saying "That's great, I hope you have an easy time!" whether the woman has told you they are going natural, or getting an elective C, or something in between, is the only good and honest response. No one needs to hear a "but" unless you are their OB and have detailed information as to their health history.
Yes, I agree that the wording of that might be a little awkward and require tweaking. The overall sentiment, though...well, I myself am childfree by choice so take what I have to say with as much salt as you like.
I can so easily imagine a woman laboring herself to exhaustion, in unbearable pain, because she has told everyone she is doing it naturally and would feel foolish or guilty if she asked for pain drugs. I can imagine a woman deciding in the middle of labor that she really does want pain drugs but she is so overwhelmed by pain at that point that she can't think clearly about the possible options for pain drugs and the choice, well-meaning as it is, gets made by her husband or the doctor and it might not be the best for her. I can imagine a woman who suddenly needs a c-section who is very freaked out and panicked by the whole procedure because she didn't research it at all to know what it involved, because she was so sure she would have a natural labor and delivery.
And on the other hand, I can imagine that if a woman is prepared for all the possible ways childbirth can take strange turns, and really wants a natural labor but has researched possible methods for pain relief to know what she would be most comfortable asking for and at what point in the delivery, and what exactly a c-section involves and is like, she would feel more in control of the process, and her labor would go more smoothly both physically and mentally, and both she and her baby would be much better off.
So, I wonder if there is an e-hell approved way to say "It is very admirable that you have put so much thought into your birth plan, but please understand that every labor is different and you might find yourself in an unexpected situation. Please, please do not feel inferior or guilty or ashamed if you decide to take pain drugs or if you need a c-section. It doesn't mean you are a hypocrite or a bad or weak person or that you don't truly love your baby or you are a bad mother. Whatever happens, I wish you the very best."
But this might be a situation where it's only appropriate to say this if you are a close relative, and if it's just some random co-worker carrying on, you really should just say "That's great! I wish you the best!". In at least some situations, though, I think it would be such a kindness to the mother to let her know that "natural" childbirth is not the only acceptable method for delivery and that no one has the right to judge her for either choosing something different in advance or changing her mind in the middle of labor.