I believe the standard response when you don't feel able to write a strong recommendation letter is to say, "I don't feel I know your work well enough to write a strong recommendation, and you would be best served by finding someone who knows your work better than I do." Or something to that effect.
When a student receives this somewhat coded response, she can say Thanks anyway, and approach someone else, or she can try a little harder with you. At which point you could either stand your ground, or relent and write her a lukewarm letter.
What complicates your current situation is that you already said yes, and now you are trying to figure out if you can, and should, back-pedal.
The options available to you, that I can see, are:
Back-pedal, and send her the above message. You could apologize for sending an incomplete response previously, having glanced at her email in a cursory way without really taking it in before responding. Or whatever excuse you care to give.
Tell a white lie. Apologize and explain that your week has gotten more complicated than you anticipated, and you're not going to have time to do her form. If you choose this one, the email you send must be very brief and apologetic, and should contain a couple of spelling mistakes, to look authentic.
Invent an illness or an illness in your family that prevents you from making her deadline. This is a variant of option 2.
Tell her honestly that when you agreed to do it, you thought the form was going to be shorter than it turned out to be. Explain that you had not opened the attachment until now. Point out the "comments" question. Explain that you don't know her well enough to tackle that question, or explain that you don't have enough time to do anything more than check off boxes and fill out short response questions.
Proceed with filling out the form, knowing that your recommendation will not be very strong. Do not say anything to the student about how lukewarm your recommendation will be. Remember that this is not the only program she will ever apply to, and your responses in the form are unlikely to change the outcome of her application one way or the other.
As you are considering your options, you may want to try to apply the Golden Rule. In other words, what would you want Prof. Sana to do if you were Prof. Sana's less-than-stellar student?
What do you think would be most helpful to this student in the long term? You know more about this than we do, because one can only fit so much into a post, about the student's potential, temperament, ambitions, reasons for a mediocre performance, and hopes and dreams for herself.