Indeed; had there been human observers at the time when the split between chordates and [whatever else there was], they would almost certainly have classified the new organism Somethingia Chordata - i.e. they would have viewed it as a speciation event, even though it looks from here like a branch at phylum level.
The current thought, as I understand it, is that chordates are decended from an invertebrate species that, as juveniles, have a primitive spinal cord which they then lose as adults. This is an example of Neoteny, I understand - the phenomenon where adult members of one species posess traits that are found only in the juveniles of a closely related species. (Certain human characteristics display the same neoteny to chimp juveniles.)
This, if a creationist had been observing the event along with the scientist, he or she would have likely countered "Not speciation at all, but rather a degenerate form of this invertebrate. It stubbornly refuses to become an adult." Or something similar. I think this example shows how creationist demands for evidence of new taxa is a kind of loaded question.