This sentence is fine if you perceive the speaker is thinking in a particular way: "She is tall but smart" = even though she is tall (and in this instance perceived as a negative (quality) for the speaker), it is offset by the fact that she is smart.

The first sentence does not make much sense. It means that she is tall, and in spite of that she is still smart. However we know that being tall does not stop you being smart, so the sentence is not right.