I don't think this is an issue. The only thing that matters from a licensing perspective is whether the libc is legally a derived work of the kernel (or vice versa). If they are not currently derived works being distributed on separate sites, then I don't see how changing them to be distributed on the same site causes them to become derived works. The interface between the kernel and libc will continue to be the syscall interface + header files, just as today.
Of course we cannot have a libc which is licensed under the GPL. It must be the LGPL, or else something weaker. Otherwise no one will ever use it.