I think Isabella does care for her father. We are told in chapter 11 that

...the ways of Hartfield and the feelings of her father were so respected by Mrs. John Knightley, that in spite of maternal solicitude for the immediate enjoyment of her little ones, and for their having instantly all the liberty and attendance, all the eating and drinking, and sleeping and playing, which they could possibly wish for, without the smallest delay, the children were never allowed to be long a disturbance to him, either in themselves or in any restless attendance on them.

So Isabella is willing to put her father's peace above even indulging her children.

I think the reason that Isabella does not try to keep the conversation with her father on an even knell is that she's not as smart as her younger sister. Mr Knightley said in chapter 5 Emma is spoiled by being the cleverest of her family. At ten years old, she had the misfortune of being able to answer questions which puzzled her sister at seventeen.