The suitability of skipping Pre-algebra is heavily dependent on your school's curriculum and teacher. I would not let my kids skip any course from Pre-Algebra on up but the scale may in fact tilt the other way at your DD's school. For DS, the Pre-Algebra course established a strong foundation in Geometry and Trigonometry, his relatively weaker areas since he is not a visual spatial kid. Even though elementary algebra and elementary geometry are incorporated starting with 1st grade, it was reassuring to see that DS can handle real Geometry and Trigonometry. On the other hand, it may be characterized as Geometry-lite and Trigonometry-lite and arguably will be repeated later in Geometry and Trigonometry. So it comes down to your philosophy - do you think that it is beneficial or harmful for kids to see/practice concepts that they have already seen in a previous course. I tend to answer somewhat beneficial for my own kids, who often learn too fast and may sometimes run the risk of forgetting concepts/procedures that they covered in a flash.

By the way, I had DS take the AOPS Are You Ready? test for Algebra. The results showed that DS was ready although we ultimately elected to only accelerate to Pre-Algebra for a number of other reasons including the Geometry/spatial issues.

On the other hand, I question the vigor of a course that uses Khan Academy as instruction unless the teacher will develop/introduce her own instructional material as well. While I think Khan Academy is wonderful as a supplement and it's free, it is gear toward the "every man" and not gear toward gifted at all. If the Pre-Algebra course is low level and only cover "algebra-lite" topics (as indicated by some of the other posters' curriculum) or your DD is strong with visual spatial tasks, then it may make sense to skip Pre-algebra.

Since this is a new school, the best way to advocate is to have her ace their readiness and end of course tests. I would provide outside testing only if you think that it is necessary to unlock the door to their readiness and end of course tests.