In phylogeny, genomic is just another tool. The point is that turtles are os course animals, but they do branch off of different reptile groups if you look at morphological evidence (which includes fossil data) or at molecular (genetic) evidence (which only includes extant species). This is not something frequent, as usually molecular evidence tends to strengthen previous morphologically established evolutionary relationships. And even though molecularists are more numerous today, their methods are neither better or worse than anatomy.
Phylogeny is not as straightforward as some people make it seem, and especially molecular phylogeny tends to rely on abstract concepts that can’t always be backed up by biological evidence (I’m not saying it’s wrong, it’s very often very good, juste that a lot of people doing it do not understand the way it works, and thus can’t examine the process critically).
And so turtles’ origin are still very much an active debate!