It sounds like a good idea. After all, we all know stories of bright people or great hackers that felt academic education wasn't for them and followed a different, successful path. And after all, Xavier Niel should know, being a such a successful entrepreneur.
Well, I think he's wrong for several reasons.
1 - even though he says otherwise, conventionally CS is already taught largely with programming projects.
2 - this field has became so complex that IMHO it's increasingly difficult to escape some theoretical knowledge. And actually, 42 curriculum has plenty of it. It's not clear how it's gonna be taught, and I can't see how a student that failed to learn let say Automata theory, linear algebra and Fourier transforms at university would succeed just because he's now supposed to learn by himself.
3 - I think teaching with projects still requires a lot of preparation and supervision from the teachers, and last time I checked, 42 didn't have that kind of resources. For instance, you can't just ask 800 students to write a shell (and learn UNIX and C in the process) by leaving them on their own for a month. Of course, some will do it, but most won't. I doubt they manage to find 800 john carmack.