Containing fragments doesn't mean this is a dire wolf, or does it? Biological categories like species are fuzzy anyway. There is tremendous variation within each species. But where do you draw a line? It's something that perhaps has more in common with a dire wolf than extant wolves. Maybe it looks like one. Does it act like one? Do we have any way of knowing?
... which begs the question: when you're doing Bene-Gesserit-style eugenics on tortoises to get the perfect specimens, what's the nature of the nature you're trying to preserve?
Humans cannot interact with the natural world without changing it, because it is the nature of life (and human life in particular) to change things. The question isn't how we don't make an impact; it's how do we manage that impact responsibly?
(I have no idea if breeding dire-wolf-alikes with genetic modification is responsible or not. Let me know if they get out of the lab and become an invasive species, I think).